diff --git a/drop/config/SampleAnnotation.py b/drop/config/SampleAnnotation.py
index 0bdfc7d2..b473d34f 100644
--- a/drop/config/SampleAnnotation.py
+++ b/drop/config/SampleAnnotation.py
@@ -9,7 +9,7 @@
 
 
 class SampleAnnotation:
-    FILE_TYPES = ["RNA_BAM_FILE", "DNA_VCF_FILE", "GENE_COUNTS_FILE"]
+    FILE_TYPES = ["RNA_BAM_FILE", "DNA_VCF_FILE", "GENE_COUNTS_FILE", "SPLICE_COUNTS_DIR"]
     SAMPLE_ANNOTATION_COLUMNS = FILE_TYPES + [
         "RNA_ID", "DNA_ID", "DROP_GROUP", "GENE_ANNOTATION",
         "PAIRED_END", "COUNT_MODE", "COUNT_OVERLAPS", "STRAND", "GENOME"
@@ -32,6 +32,7 @@ def __init__(self, file, root, genome):
         self.dnaIDs = self.createGroupIds(file_type="DNA_VCF_FILE", sep=',')
         # external counts
         self.extGeneCountIDs = self.createGroupIds(file_type="GENE_COUNTS_FILE", sep=',')
+        self.extSpliceCountIDs = self.createGroupIds(file_type="SPLICE_COUNTS_DIR", sep=',')
 
     def parse(self, sep='\t'):
         """
@@ -80,10 +81,12 @@ def createSampleFileMapping(self):
             columns: [ID | ASSAY | FILE_TYPE | FILE_PATH ]
         """
 
-        assay_mapping = {'RNA_ID': ['RNA_BAM_FILE', 'GENE_COUNTS_FILE'], 'DNA_ID': ['DNA_VCF_FILE']}
+        assay_mapping = {'RNA_ID': ['RNA_BAM_FILE', 'GENE_COUNTS_FILE', 'SPLICE_COUNTS_DIR'], 'DNA_ID': ['DNA_VCF_FILE']}
         assay_subsets = []
         for id_, file_types in assay_mapping.items():
             for file_type in file_types:
+                if file_type not in self.sa.columns:
+                    continue
                 df = self.annotationTable[[id_, file_type]].dropna().drop_duplicates().copy()
                 df.rename(columns={id_: 'ID', file_type: 'FILE_PATH'}, inplace=True)
                 df['ASSAY'] = id_
@@ -249,17 +252,24 @@ def getGenomes(self, value, group, file_type="RNA_ID",
 
         return {sample_id: value for sample_id in subset[file_type].tolist()}
 
-    def getImportCountFiles(self, annotation, group, file_type="GENE_COUNTS_FILE",
-                            annotation_key="GENE_ANNOTATION", group_key="DROP_GROUP",exact_match = True):
+    def getImportCountFiles(self, annotation, group, file_type: str = "GENE_COUNTS_FILE",
+                            annotation_key: str = "GENE_ANNOTATION", group_key: str = "DROP_GROUP", 
+                            exact_match = True, asSet: bool = True):
         """
-        :param annotation: annotation name as specified in config and GENE_ANNOTATION column
-        :param group: a group of the DROP_GROUP column. exact match is passed to subsetter, false allows for substring matching
+        :param annotation: annotation name as specified in config and GENE_ANNOTATION column. Can be None
+        :param group: a group of the DROP_GROUP column.
+        :param exact_match: exact_match is passed to subsetter, False allows for substring matching
+        :param asSet: if True, default, a set is returned else a list. 
         :return: set of unique external count file names
         """
+        
         #subset for the annotation_key in the annotation group and the group_key in the group
-        subset = self.subsetSampleAnnotation(annotation_key, annotation,exact_match=exact_match)
-        subset = self.subsetSampleAnnotation(group_key, group, subset,exact_match=exact_match)
-        return set(subset[file_type].tolist())
+        subset = self.subsetSampleAnnotation(annotation_key, annotation, exact_match=exact_match)
+        subset = self.subsetSampleAnnotation(group_key, group, subset, exact_match=exact_match)
+        ans = subset[file_type].tolist()
+        if asSet:
+            ans = set(ans)
+        return ans
 
     def getRow(self, column, value):
         sa = self.annotationTable
@@ -277,7 +287,8 @@ def getGroupedIDs(self, assays):
         Get group to IDs mapping
         :param assays: list of or single assay the IDs should be from. Can be file_type or 'RNA'/'DNA'
         """
-        assays = [assays] if isinstance(assays, str) else assays
+        if isinstance(assays, str):
+            assays = [assays]
         groupedIDs = defaultdict(list)
         for assay in assays:
             if "RNA" in assay:
@@ -286,6 +297,8 @@ def getGroupedIDs(self, assays):
                 groupedIDs.update(self.dnaIDs)
             elif "GENE_COUNT" in assay:
                 groupedIDs.update(self.extGeneCountIDs)
+            elif "SPLICE_COUNT" in assay:
+                groupedIDs.update(self.extSpliceCountIDs)
             else:
                 raise ValueError(f"'{assay}' is not a valid assay name")
         return groupedIDs
diff --git a/drop/config/submodules/AberrantSplicing.py b/drop/config/submodules/AberrantSplicing.py
index 4d3f3651..d5954cb8 100644
--- a/drop/config/submodules/AberrantSplicing.py
+++ b/drop/config/submodules/AberrantSplicing.py
@@ -1,3 +1,6 @@
+import numpy as np
+import pandas as pd
+
 from snakemake.io import expand
 
 from drop import utils
@@ -43,10 +46,10 @@ def getSplitCountFiles(self, dataset):
         :return: list of files
         """
         ids = self.sampleAnnotation.getIDsByGroup(dataset, assay="RNA")
-        file_stump = self.processedDataDir / "aberrant_splicing" / "datasets" / "cache" / f"raw-{dataset}" / \
-                     "sample_tmp" / "splitCounts"
-        done_files = str(file_stump / "sample_{sample_id}.done")
-        return expand(done_files, sample_id=ids)
+        file_stump = self.processedDataDir / "aberrant_splicing" / "datasets" / "cache"
+        count_file = str(file_stump / "splitCounts-{sample_id}.RDS")
+        return expand(count_file, sample_id=ids)
+
 
     def getNonSplitCountFiles(self, dataset):
         """
@@ -55,7 +58,25 @@ def getNonSplitCountFiles(self, dataset):
         :return: list of files
         """
         ids = self.sampleAnnotation.getIDsByGroup(dataset, assay="RNA")
-        file_stump = self.processedDataDir / "aberrant_splicing" / "datasets" / "cache" / f"raw-{dataset}" / \
-                     "sample_tmp" / "nonSplitCounts"
-        done_files = str(file_stump / "sample_{sample_id}.done")
+        file_stump = self.processedDataDir / "aberrant_splicing" / "datasets" / \
+                     "cache" / "nonSplicedCounts" / f"raw-{dataset}" 
+        done_files = str(file_stump / "nonSplicedCounts-{sample_id}.h5")
         return expand(done_files, sample_id=ids)
+
+
+    def getExternalCounts(self, group: str, fileType: str = "k_j_counts"):
+        """
+        Get externally provided splice count data dir based on the given group.
+        If a file type is given the corresponding file within the folder is returned. 
+        :param group: DROP group name from wildcard
+        :param fileType: name of the file without extension which is to be returned
+        :return: list of directories or files
+        """
+        ids = self.sa.getIDsByGroup(group, assay="SPLICE_COUNT")
+        extCountFiles = self.sa.getImportCountFiles(annotation=None, group=group, 
+                file_type="SPLICE_COUNTS_DIR", asSet=False)
+        if fileType is not None:
+            extCountFiles = np.asarray(extCountFiles)[pd.isna(extCountFiles) == False].tolist()
+            extCountFiles = [x + "/" + fileType + ".tsv.gz" for x in extCountFiles]
+        return extCountFiles
+    
diff --git a/drop/demo/config_relative.yaml b/drop/demo/config_relative.yaml
index f79852d0..ca9cc6c9 100755
--- a/drop/demo/config_relative.yaml
+++ b/drop/demo/config_relative.yaml
@@ -17,6 +17,7 @@ exportCounts:
   excludeGroups:
     - mae
     - import_exp
+    - fraser_ex
 
 aberrantExpression:
     run: true
@@ -36,6 +37,7 @@ aberrantSplicing:
     run: true
     groups:
       - fraser
+      - fraser_ex
     recount: true
     longRead: false
     keepNonStandardChrs: true
diff --git a/drop/demo/sample_annotation_relative.tsv b/drop/demo/sample_annotation_relative.tsv
old mode 100755
new mode 100644
index 0da07a27..8f6d12ba
--- a/drop/demo/sample_annotation_relative.tsv
+++ b/drop/demo/sample_annotation_relative.tsv
@@ -1,23 +1,25 @@
-RNA_ID	RNA_BAM_FILE	DNA_VCF_FILE	DNA_ID	DROP_GROUP	PAIRED_END	COUNT_MODE	COUNT_OVERLAPS	STRAND	HPO_TERMS	GENE_COUNTS_FILE	GENE_ANNOTATION	GENOME
-HG00096.1.M_111124_6	Data/rna_bam/HG00096.1.M_111124_6_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00096	outrider,mae	TRUE	IntersectionStrict	TRUE	no	HP:0009802,HP:0010896
-HG00103.4.M_120208_3	Data/rna_bam/HG00103.4.M_120208_3_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00103	outrider,mae	TRUE	IntersectionStrict	TRUE	no	HP:0004582,HP:0031959
-HG00106.4.M_120208_5	Data/rna_bam/HG00106.4.M_120208_5_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00106	outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0002895,HP:0006731
-HG00111.2.M_111215_4	Data/rna_bam/HG00111.2.M_111215_4_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00111	outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0100491,HP:0100871
-HG00116.2.M_120131_1	Data/rna_bam/HG00116.2.M_120131_1_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00116	outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0030613,HP:0012767
-HG00126.1.M_111124_8	Data/rna_bam/HG00126.1.M_111124_8_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00126	outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0000290,HP:0000293
-HG00132.2.M_111215_4	Data/rna_bam/HG00132.2.M_111215_4_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00132	outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0006489,HP:0006490
-HG00149.1.M_111124_6	Data/rna_bam/HG00149.1.M_111124_6_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00149	outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0000014,HP:0000020,HP:0032663
-HG00150.4.M_120208_7	Data/rna_bam/HG00150.4.M_120208_7_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00150	outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0030809,HP:0006144
-HG00176.4.M_120208_2	Data/rna_bam/HG00176.4.M_120208_2_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00176	outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0005215,HP:0010234
-HG00096.1.M_111124_6_trunc	Data/rna_bam/HG00096.1.M_111124_6_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00096	fraser	TRUE	IntersectionStrict	TRUE	no	HP:0009802,HP:0010896
-HG00103.4.M_120208_3_trunc	Data/rna_bam/HG00103.4.M_120208_3_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00103	fraser	TRUE	IntersectionStrict	TRUE	no	HP:0004582,HP:0031959
-HG00106.4.M_120208_5_trunc	Data/rna_bam/HG00106.4.M_120208_5_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00106	fraser	TRUE	IntersectionStrict	TRUE	no	HP:0002895,HP:0006731
-HG00111.2.M_111215_4_trunc	Data/rna_bam/HG00111.2.M_111215_4_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00111	fraser	TRUE	IntersectionStrict	TRUE	no	HP:0100491,HP:0100871
-HG00116.2.M_120131_1_trunc	Data/rna_bam/HG00116.2.M_120131_1_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00116	fraser	TRUE	IntersectionStrict	TRUE	no	HP:0030613,HP:0012767
-HG00126.1.M_111124_8_trunc	Data/rna_bam/HG00126.1.M_111124_8_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00126	fraser	TRUE	IntersectionStrict	TRUE	no	HP:0000290,HP:0000293
-HG00132.2.M_111215_4_trunc	Data/rna_bam/HG00132.2.M_111215_4_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00132	fraser	TRUE	IntersectionStrict	TRUE	no	HP:0006489,HP:0006490
-HG00149.1.M_111124_6_trunc	Data/rna_bam/HG00149.1.M_111124_6_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00149	fraser	TRUE	IntersectionStrict	TRUE	no	HP:0000014,HP:0000020,HP:0032663
-HG00150.4.M_120208_7_trunc	Data/rna_bam/HG00150.4.M_120208_7_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00150	fraser	TRUE	IntersectionStrict	TRUE	no	HP:0030809,HP:0006144
-HG00176.4.M_120208_2_trunc	Data/rna_bam/HG00176.4.M_120208_2_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00176	fraser	TRUE	IntersectionStrict	TRUE	no	HP:0005215,HP:0010234
-HG00178.4.M_120208_8				import_exp						Data/external_geneCounts.tsv.gz	v29
-HG00181.4.M_120208_4				import_exp						Data/external_geneCounts.tsv.gz	v29
+RNA_ID	RNA_BAM_FILE	DNA_VCF_FILE	DNA_ID	DROP_GROUP	PAIRED_END	COUNT_MODE	COUNT_OVERLAPS	STRAND	HPO_TERMS	GENE_COUNTS_FILE	GENE_ANNOTATION	GENOME	SPLICE_COUNTS_DIR
+HG00096.1.M_111124_6	Data/rna_bam/HG00096.1.M_111124_6_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00096	outrider,mae	TRUE	IntersectionStrict	TRUE	no	HP:0009802,HP:0010896				
+HG00103.4.M_120208_3	Data/rna_bam/HG00103.4.M_120208_3_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00103	outrider,mae	TRUE	IntersectionStrict	TRUE	no	HP:0004582,HP:0031959				
+HG00106.4.M_120208_5	Data/rna_bam/HG00106.4.M_120208_5_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00106	outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0002895,HP:0006731				
+HG00111.2.M_111215_4	Data/rna_bam/HG00111.2.M_111215_4_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00111	outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0100491,HP:0100871				
+HG00116.2.M_120131_1	Data/rna_bam/HG00116.2.M_120131_1_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00116	outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0030613,HP:0012767				
+HG00126.1.M_111124_8	Data/rna_bam/HG00126.1.M_111124_8_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00126	outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0000290,HP:0000293				
+HG00132.2.M_111215_4	Data/rna_bam/HG00132.2.M_111215_4_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00132	outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0006489,HP:0006490				
+HG00149.1.M_111124_6	Data/rna_bam/HG00149.1.M_111124_6_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00149	outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0000014,HP:0000020,HP:0032663				
+HG00150.4.M_120208_7	Data/rna_bam/HG00150.4.M_120208_7_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00150	fraser_ex,outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0030809,HP:0006144				
+HG00176.4.M_120208_2	Data/rna_bam/HG00176.4.M_120208_2_chr21.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00176	fraser_ex,outrider,import_exp	TRUE	IntersectionStrict	TRUE	no	HP:0005215,HP:0010234				
+HG00096.1.M_111124_6_trunc	Data/rna_bam/HG00096.1.M_111124_6_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00096	fraser,fraser_ex	TRUE	IntersectionStrict	TRUE	no	HP:0009802,HP:0010896				
+HG00103.4.M_120208_3_trunc	Data/rna_bam/HG00103.4.M_120208_3_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00103	fraser,fraser_ex	TRUE	IntersectionStrict	TRUE	no	HP:0004582,HP:0031959				
+HG00106.4.M_120208_5_trunc	Data/rna_bam/HG00106.4.M_120208_5_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00106	fraser,fraser_ex	TRUE	IntersectionStrict	TRUE	no	HP:0002895,HP:0006731				
+HG00111.2.M_111215_4_trunc	Data/rna_bam/HG00111.2.M_111215_4_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00111	fraser,fraser_ex	TRUE	IntersectionStrict	TRUE	no	HP:0100491,HP:0100871				
+HG00116.2.M_120131_1_trunc	Data/rna_bam/HG00116.2.M_120131_1_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00116	fraser,fraser_ex	TRUE	IntersectionStrict	TRUE	no	HP:0030613,HP:0012767				
+HG00126.1.M_111124_8_trunc	Data/rna_bam/HG00126.1.M_111124_8_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00126	fraser,fraser_ex	TRUE	IntersectionStrict	TRUE	no	HP:0000290,HP:0000293				
+HG00132.2.M_111215_4_trunc	Data/rna_bam/HG00132.2.M_111215_4_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00132	fraser,fraser_ex	TRUE	IntersectionStrict	TRUE	no	HP:0006489,HP:0006490				
+HG00149.1.M_111124_6_trunc	Data/rna_bam/HG00149.1.M_111124_6_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00149	fraser,fraser_ex	TRUE	IntersectionStrict	TRUE	no	HP:0000014,HP:0000020,HP:0032663				
+HG00150.4.M_120208_7_trunc	Data/rna_bam/HG00150.4.M_120208_7_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00150	fraser	TRUE	IntersectionStrict	TRUE	no	HP:0030809,HP:0006144				
+HG00176.4.M_120208_2_trunc	Data/rna_bam/HG00176.4.M_120208_2_chr21.bam_trunc.bam	Data/dna_vcf/demo_chr21.vcf.gz	HG00176	fraser	TRUE	IntersectionStrict	TRUE	no	HP:0005215,HP:0010234				
+HG00178.4.M_120208_8				import_exp						Data/external_count_data/geneCounts.tsv.gz	v29		
+HG00181.4.M_120208_4				fraser_ex,import_exp						Data/external_count_data/geneCounts.tsv.gz	v29		Data/external_count_data
+HG00191.3.M_120208_3				fraser_ex									Data/external_count_data
+HG00201.1.M_120208_6				fraser_ex									Data/external_count_data
diff --git a/drop/download_data.sh b/drop/download_data.sh
index ba2ac064..a48faad4 100644
--- a/drop/download_data.sh
+++ b/drop/download_data.sh
@@ -2,9 +2,10 @@
 set -e
 
 # get data
-resource_url="https://www.cmm.in.tum.de/public/paper/drop_analysis/resource.tar.gz"
-tmpdir="$(dirname "$(mktemp)")"
-wget -nc -P $tmpdir $resource_url
+resource_url="https://www.cmm.in.tum.de/public/paper/drop_analysis/resource_splice_merge.tar.gz"
+tmpdir=$(dirname "$(mktemp -u)")
+wget -nc -O "$tmpdir/resource.tar.gz" "$resource_url"
+
 mkdir -p Data
 if [ -z "$(ls Data)" ]; then
 	tar -zxvf "$tmpdir/resource.tar.gz" -C .
diff --git a/drop/modules/aberrant-splicing-pipeline/Counting/00_define_datasets_from_anno.R b/drop/modules/aberrant-splicing-pipeline/Counting/00_define_datasets_from_anno.R
index 72e17db9..b8a46381 100644
--- a/drop/modules/aberrant-splicing-pipeline/Counting/00_define_datasets_from_anno.R
+++ b/drop/modules/aberrant-splicing-pipeline/Counting/00_define_datasets_from_anno.R
@@ -5,9 +5,7 @@
 #'  log:
 #'    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "00_defineDataset.Rds")`'
 #'  params:
-#'    - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
 #'    - ids: '`sm lambda w: sa.getIDsByGroup(w.dataset, assay="RNA")`'
-#'    - fileMappingFile: '`sm cfg.getRoot() + "/file_mapping.csv"`'
 #'  input:
 #'    - sampleAnnoFile: '`sm config["sampleAnnotation"]`'
 #'  output:
@@ -23,30 +21,30 @@
 #'---
 
 saveRDS(snakemake, snakemake@log$snakemake)
-source(snakemake@params$setup, echo=FALSE)
+suppressPackageStartupMessages(library(data.table))
 
 #+ input
 outFile       <- snakemake@output$colData
 annoFile      <- snakemake@input$sampleAnnoFile
-fileMapFile   <- snakemake@params$fileMapping
 
 #+ dataset name
 
 name <- snakemake@wildcards$dataset
 anno    <- fread(annoFile)
-mapping <- fread(fileMapFile)
 
 subset_ids <- snakemake@params$ids
 annoSub <- anno[RNA_ID %in% subset_ids]
-colData <- merge(
-    annoSub[,.(sampleID = RNA_ID, STRAND, PAIRED_END)],
-    mapping[FILE_TYPE == "RNA_BAM_FILE", .(sampleID=ID, bamFile=FILE_PATH)])
+setnames(annoSub, "RNA_ID", "sampleID")
+setnames(annoSub, "RNA_BAM_FILE", "bamFile")
+setnames(annoSub, "PAIRED_END", "pairedEnd")
+setcolorder(annoSub, unique(c("sampleID", "STRAND", "pairedEnd", "bamFile"), 
+        colnames(annoSub)))
 
 #'
 #' ## Dataset: `r name`
 #'
 #+ echo=FALSE
-finalTable <- colData
+finalTable <- annoSub
 
 #'
 #' ## Final sample table `r name`
@@ -55,4 +53,4 @@ finalTable <- colData
 DT::datatable(finalTable, options=list(scrollX=TRUE))
 
 dim(finalTable)
-write_tsv(finalTable, file=outFile)
+write.table(x=finalTable, file=outFile, quote=FALSE, sep='\t', row.names=FALSE)
diff --git a/drop/modules/aberrant-splicing-pipeline/Counting/01_0_countRNA_init.R b/drop/modules/aberrant-splicing-pipeline/Counting/01_0_countRNA_init.R
index c54948ee..9c40fa14 100644
--- a/drop/modules/aberrant-splicing-pipeline/Counting/01_0_countRNA_init.R
+++ b/drop/modules/aberrant-splicing-pipeline/Counting/01_0_countRNA_init.R
@@ -4,37 +4,32 @@
 #' wb:
 #'  log:
 #'    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "01_0_init.Rds")`'
-#'  params:
-#'   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
-#'   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'
 #'  input:
 #'    - colData: '`sm cfg.getProcessedDataDir() + 
 #'                    "/aberrant_splicing/annotations/{dataset}.tsv"`'
 #'  output:
-#'   - fdsobj:  '`sm cfg.getProcessedDataDir() + 
-#'                   "/aberrant_splicing/datasets/savedObjects/raw-{dataset}/fds-object.RDS"`'
-#'   - done_fds: '`sm cfg.getProcessedDataDir() + 
-#'                "/aberrant_splicing/datasets/cache/raw-{dataset}/fds.done" `'
+#'   - fds_init:  '`sm cfg.getProcessedDataDir() + 
+#'                   "/aberrant_splicing/datasets/savedObjects/raw-{dataset}/fds-init.done"`'
 #'  type: script
 #'---
 
 saveRDS(snakemake, snakemake@log$snakemake)
-source(snakemake@params$setup, echo=FALSE)
+suppressPackageStartupMessages(library(FRASER))
 
-dataset    <- snakemake@wildcards$dataset
+# input
+dataset     <- snakemake@wildcards$dataset
 colDataFile <- snakemake@input$colData
-workingDir <- snakemake@params$workingDir
-params <- snakemake@config$aberrantSplicing
+fds_init    <- snakemake@output$fds_init
+params      <- snakemake@config$aberrantSplicing
 
 # Create initial FRASER object
 col_data <- fread(colDataFile)
 
 fds <- FraserDataSet(colData = col_data,
-                     workingDir = workingDir,
+                     workingDir = dirname(dirname(dirname(fds_init))),
                      name       = paste0("raw-", dataset))
 
-# Add paired end and strand specificity to the fds
-pairedEnd(fds) <- colData(fds)$PAIRED_END
+# Add strand specificity to the fds
 strandSpecific(fds) <- 'no'
 if(uniqueN(colData(fds)$STRAND) == 1){
   strandSpecific(fds) <- unique(colData(fds)$STRAND)
@@ -45,4 +40,4 @@ fds <- saveFraserDataSet(fds)
 
 message(date(), ": FRASER object initialized for ", dataset)
 
-file.create(snakemake@output$done_fds)
+file.create(fds_init)
diff --git a/drop/modules/aberrant-splicing-pipeline/Counting/01_1_countRNA_splitReads_samplewise.R b/drop/modules/aberrant-splicing-pipeline/Counting/01_1_countRNA_splitReads_samplewise.R
index 5da348af..6659f467 100644
--- a/drop/modules/aberrant-splicing-pipeline/Counting/01_1_countRNA_splitReads_samplewise.R
+++ b/drop/modules/aberrant-splicing-pipeline/Counting/01_1_countRNA_splitReads_samplewise.R
@@ -3,51 +3,64 @@
 #' author: Luise Schuller
 #' wb:
 #'  log:
-#'    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "splitReads" / "{sample_id}.Rds")`'
+#'    - snakemake: '`sm str(tmp_dir / "AS" / "splitReads" / "{sampleID}.Rds")`'
 #'  params:
-#'   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
-#'   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'
+#'    - COUNT_PARAMS: '`sm lambda w: cfg.AE.getCountParams(w.sampleID)`'
 #'  input:
-#'   - done_fds: '`sm cfg.getProcessedDataDir() + 
-#'                "/aberrant_splicing/datasets/cache/raw-{dataset}/fds.done"`'
+#'    - sample_bam: '`sm lambda w: sa.getFilePath(w.sampleID, file_type="RNA_BAM_FILE") `'
 #'  output:
-#'   - done_sample_splitCounts: '`sm cfg.getProcessedDataDir() + 
-#'                "/aberrant_splicing/datasets/cache/raw-{dataset}"
-#'                +"/sample_tmp/splitCounts/sample_{sample_id}.done"`'
+#'    - sample_splitCounts: '`sm cfg.getProcessedDataDir() + 
+#'                   "/aberrant_splicing/datasets/cache/splitCounts-{sampleID}.RDS"`'
 #'  threads: 3
 #'  type: script
 #'---
 
 saveRDS(snakemake, snakemake@log$snakemake)
-source(snakemake@params$setup, echo=FALSE)
-library(BSgenome)
+suppressPackageStartupMessages({
+  library(FRASER)
+  library(BSgenome)
+})
 
-dataset    <- snakemake@wildcards$dataset
-workingDir <- snakemake@params$workingDir
+sampleID   <- snakemake@wildcards$sampleID
+sample_bam <- snakemake@input$sample_bam
+fds_init   <- snakemake@input$fds_init
+out_rds    <- snakemake@output$sample_splitCounts
 params <- snakemake@config$aberrantSplicing
 genomeAssembly <- snakemake@config$genomeAssembly
+strand <- snakemake@params$COUNT_PARAMS$STRAND
+paired <- snakemake@params$COUNT_PARAMS$PAIRED_END
+coldata <- fread(snakemake@config$sampleAnnotation)[RNA_ID == sampleID]
 
-# Read FRASER object
-fds <- loadFraserDataSet(dir=workingDir, name=paste0("raw-", dataset))
 
-# Get sample id from wildcard
-sample_id <- snakemake@wildcards[["sample_id"]]
+# Get strand specificity of sample ('' does not exists in switch -> x_...)
+strand <- switch(paste0("x_", tolower(strand)),
+        'x_' = 0L,
+        'x_no' = 0L,
+        'x_unstranded' = 0L,
+        'x_yes' = 1L,
+        'x_stranded' = 1L,
+        'x_reverse' = 2L,
+        stop("Strand parameter not known! It was: '", strand, "'."))
 
 # If data is not strand specific, add genome info
 genome <- NULL
-if(strandSpecific(fds) == 0){
+if(strand == 0){
   genome <- getBSgenome(genomeAssembly)
 }
 
 # Count splitReads for a given sample id
-sample_result <- countSplitReads(sampleID = sample_id, 
-                                 fds = fds,
-                                 NcpuPerSample = snakemake@threads,
-                                 recount = params$recount,
-                                 keepNonStandardChromosomes = params$keepNonStandardChrs,
-                                 genome = genome)
+sample_result <- countSplitReads(
+    sampleID = sampleID,
+    NcpuPerSample = snakemake@threads,
+    genome = genome,
+    recount = TRUE,
+    keepNonStandardChromosomes=params$keepNonStandardChrs,
+    bamfile = sample_bam,
+    pairedend = paired,
+    strandmode = strand,
+    cacheFile = out_rds,
+    scanbamparam = ScanBamParam(mapqFilter=0), 
+    coldata = coldata)
 
-message(date(), ": ", dataset, ", ", sample_id,
-        " no. splice junctions (split counts) = ", length(sample_result))
-
-file.create(snakemake@output$done_sample_splitCounts)
+message(date(), ": ", sampleID," no. splice junctions (split counts) = ", 
+    length(sample_result))
diff --git a/drop/modules/aberrant-splicing-pipeline/Counting/01_2_countRNA_splitReads_merge.R b/drop/modules/aberrant-splicing-pipeline/Counting/01_2_countRNA_splitReads_merge.R
index 1ea2a86e..28f755fe 100644
--- a/drop/modules/aberrant-splicing-pipeline/Counting/01_2_countRNA_splitReads_merge.R
+++ b/drop/modules/aberrant-splicing-pipeline/Counting/01_2_countRNA_splitReads_merge.R
@@ -4,50 +4,53 @@
 #' wb:
 #'  log:
 #'    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "01_2_splitReadsMerge.Rds")`'
-#'  params:
-#'   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
-#'   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'
-#'  threads: 20
+#'  threads: 10
 #'  input:
 #'   - sample_counts: '`sm lambda w: cfg.AS.getSplitCountFiles(w.dataset)`'
+#'   - fds_init:    '`sm cfg.getProcessedDataDir() + 
+#'                   "/aberrant_splicing/datasets/savedObjects/raw-{dataset}/fds-init.done"`'
 #'  output:
-#'   - countsJ: '`sm cfg.getProcessedDataDir() +
-#'                   "/aberrant_splicing/datasets/savedObjects/raw-{dataset}/rawCountsJ.h5"`'
+#'   - countsJ:  '`sm cfg.getProcessedDataDir() + 
+#'                    "/aberrant_splicing/datasets/savedObjects/raw-{dataset}/rawCountsJ.h5"`'
 #'   - gRangesSplitCounts: '`sm cfg.getProcessedDataDir() + 
-#'                          "/aberrant_splicing/datasets/cache/raw-{dataset}/gRanges_splitCounts.rds"`'
+#'                   "/aberrant_splicing/datasets/cache/raw-{dataset}/gRanges_splitCounts.rds"`'
 #'   - gRangesNonSplitCounts: '`sm cfg.getProcessedDataDir() + 
-#'                          "/aberrant_splicing/datasets/cache/raw-{dataset}/gRanges_NonSplitCounts.rds"`'
+#'                   "/aberrant_splicing/datasets/cache/raw-{dataset}/gRanges_NonSplitCounts.rds"`'
 #'   - spliceSites: '`sm cfg.getProcessedDataDir() + 
 #'                   "/aberrant_splicing/datasets/cache/raw-{dataset}/spliceSites_splitCounts.rds"`'
 #'  type: script
 #'---
 
 saveRDS(snakemake, snakemake@log$snakemake)
-source(snakemake@params$setup, echo=FALSE)
+suppressPackageStartupMessages(library(FRASER))
 
-dataset    <- snakemake@wildcards$dataset
-workingDir <- snakemake@params$workingDir
-params <- snakemake@config$aberrantSplicing
+# input
+dataset <- snakemake@wildcards$dataset
+fdsIn   <- file.path(dirname(snakemake@input$fds_init), "fds-object.RDS")
+params  <- snakemake@config$aberrantSplicing
 minExpressionInOneSample <- params$minExpressionInOneSample
+BPPARAM <- MulticoreParam(snakemake@threads)
 
+# Set number of threads including for DelayedArray operations
+register(BPPARAM)
+DelayedArray::setAutoBPPARAM(BPPARAM)
 
-register(MulticoreParam(snakemake@threads))
-# Limit number of threads for DelayedArray operations
-setAutoBPPARAM(MulticoreParam(snakemake@threads))
+# Force writing HDF5 files
+options(FRASER.maxSamplesNoHDF5=-1)
+options(FRASER.maxJunctionsNoHDF5=-1)
 
 # Read FRASER object
-fds <- loadFraserDataSet(dir=workingDir, name=paste0("raw-", dataset))
+fds <- loadFraserDataSet(file=fdsIn)
 
-# If samples are recounted, remove the merged ones
-splitCountsDir <- file.path(workingDir, "savedObjects", 
-                            paste0("raw-", dataset), 'splitCounts')
-if(params$recount == TRUE & dir.exists(splitCountsDir)){
-  unlink(splitCountsDir, recursive = TRUE)
+# enforce remerging if this script has to be run
+splitCountsDir <- file.path(workingDir(fds), "savedObjects", name(fds), "splitCounts")
+if(dir.exists(splitCountsDir)){
+    unlink(splitCountsDir, recursive=TRUE)
 }
 
 # Get and merge splitReads for all sample ids
-splitCounts <- getSplitReadCountsForAllSamples(fds=fds,
-                                               recount=FALSE)
+splitCounts <- getSplitReadCountsForAllSamples(fds=fds, outDir=splitCountsDir, recount=FALSE)
+
 # Extract, annotate and save granges
 splitCountRanges <- rowRanges(splitCounts)
 
@@ -65,7 +68,7 @@ splitCountRanges <- splitCountRanges[passed,]
 saveRDS(splitCountRanges, snakemake@output$gRangesNonSplitCounts)
 
 # Extract splitSiteCoodinates: extract donor and acceptor sites
-# take either filtered or full fds
+# take filtered splicesite map
 spliceSiteCoords <- FRASER:::extractSpliceSiteCoordinates(splitCountRanges, fds)
 saveRDS(spliceSiteCoords, snakemake@output$spliceSites)
 
diff --git a/drop/modules/aberrant-splicing-pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R b/drop/modules/aberrant-splicing-pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R
index c5d9e6a7..aff3f4d1 100644
--- a/drop/modules/aberrant-splicing-pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R
+++ b/drop/modules/aberrant-splicing-pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R
@@ -4,48 +4,42 @@
 #' wb:
 #'  log:
 #'    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "nonsplitReads" / "{sample_id}.Rds")`'
-#'  params:
-#'   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
-#'   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'
 #'  input:
 #'   - spliceSites: '`sm cfg.getProcessedDataDir() + 
 #'                   "/aberrant_splicing/datasets/cache/raw-{dataset}/spliceSites_splitCounts.rds"`'
+#'   - fds_init:    '`sm cfg.getProcessedDataDir() + 
+#'                   "/aberrant_splicing/datasets/savedObjects/raw-{dataset}/fds-init.done"`'
 #'  output:
-#'   - done_sample_nonSplitCounts : '`sm cfg.getProcessedDataDir() + 
-#'                   "/aberrant_splicing/datasets/cache/raw-{dataset}/sample_tmp/nonSplitCounts/sample_{sample_id}.done"`' 
+#'   - nonSplitCounts_sample : '`sm cfg.getProcessedDataDir() + 
+#'                   "/aberrant_splicing/datasets/cache/nonSplicedCounts/raw-{dataset}/nonSplicedCounts-{sample_id}.h5"`'
 #'  threads: 3
 #'  type: script
 #'---
 
 saveRDS(snakemake, snakemake@log$snakemake)
-source(snakemake@params$setup, echo=FALSE)
+suppressPackageStartupMessages(library(FRASER))
 
 dataset    <- snakemake@wildcards$dataset
-colDataFile <- snakemake@input$colData
-workingDir <- snakemake@params$workingDir
-params <- snakemake@config$aberrantSplicing
+sample_id  <- snakemake@wildcards$sample_id
+fds_init   <- snakemake@input$fds_init
+params     <- snakemake@config$aberrantSplicing
 
 # Read FRASER object
-fds <- loadFraserDataSet(dir=workingDir, name=paste0("raw-", dataset))
-
-# Get sample id from wildcard
-sample_id <- snakemake@wildcards[["sample_id"]]
-
+fds <- loadFraserDataSet(file=file.path(dirname(fds_init), "fds-object.RDS"))
 
 # Read splice site coordinates from RDS
 spliceSiteCoords <- readRDS(snakemake@input$spliceSites)
 
 # Count nonSplitReads for given sample id
 sample_result <- countNonSplicedReads(sample_id,
-                                      splitCountRanges = NULL,
-                                      fds = fds,
-                                      NcpuPerSample = snakemake@threads,
-                                      minAnchor=5,
-                                      recount=params$recount,
-                                      spliceSiteCoords=spliceSiteCoords,
-                                      longRead=params$longRead)
+        splitCountRanges = NULL,
+        fds = fds,
+        NcpuPerSample = snakemake@threads,
+        minAnchor=5,
+        # TODO should be TRUE in the future as snakemake is checking this
+        recount=params$recount,
+        spliceSiteCoords=spliceSiteCoords,
+        longRead=params$longRead)
 
 message(date(), ": ", dataset, ", ", sample_id,
         " no. splice junctions (non split counts) = ", length(sample_result))
-
-file.create(snakemake@output$done_sample_nonSplitCounts)
diff --git a/drop/modules/aberrant-splicing-pipeline/Counting/01_4_countRNA_nonSplitReads_merge.R b/drop/modules/aberrant-splicing-pipeline/Counting/01_4_countRNA_nonSplitReads_merge.R
index 83c48939..7ceacd00 100644
--- a/drop/modules/aberrant-splicing-pipeline/Counting/01_4_countRNA_nonSplitReads_merge.R
+++ b/drop/modules/aberrant-splicing-pipeline/Counting/01_4_countRNA_nonSplitReads_merge.R
@@ -4,10 +4,7 @@
 #' wb:
 #'  log:
 #'    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "01_4_nonSplitReadsMerge.Rds")`'
-#'  params:
-#'   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
-#'   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'
-#'  threads: 20
+#'  threads: 10
 #'  input:
 #'   - sample_counts:  '`sm lambda w: cfg.AS.getNonSplitCountFiles(w.dataset)`'
 #'   - gRangesNonSplitCounts: '`sm cfg.getProcessedDataDir() + 
@@ -19,34 +16,39 @@
 #'---
 
 saveRDS(snakemake, snakemake@log$snakemake)
-source(snakemake@params$setup, echo=FALSE)
+suppressPackageStartupMessages(library(FRASER))
 
-dataset    <- snakemake@wildcards$dataset
-workingDir <- snakemake@params$workingDir
-params <- snakemake@config$aberrantSplicing
+dataset <- snakemake@wildcards$dataset
+fds_in  <- file.path(dirname(snakemake@output$countsSS), "fds-object.RDS")
+params  <- snakemake@config$aberrantSplicing
+BPPARAM <- MulticoreParam(snakemake@threads)
 
-register(MulticoreParam(snakemake@threads))
-# Limit number of threads for DelayedArray operations
-setAutoBPPARAM(MulticoreParam(snakemake@threads))
+# Set number of threads including for DelayedArray operations
+register(BPPARAM)
+DelayedArray::setAutoBPPARAM(BPPARAM)
+
+# Force writing HDF5 files
+options(FRASER.maxSamplesNoHDF5=-1)
+options(FRASER.maxJunctionsNoHDF5=-1)
 
 # Read FRASER object
-fds <- loadFraserDataSet(dir=workingDir, name=paste0("raw-", dataset))
+fds <- loadFraserDataSet(file=fds_in)
 
 # Read splice site coordinates from RDS
 splitCounts_gRanges <- readRDS(snakemake@input$gRangesNonSplitCounts)
 
 # If samples are recounted, remove the merged ones
-nonSplitCountsDir <- file.path(workingDir, "savedObjects", 
-                            paste0("raw-", dataset), 'nonSplitCounts')
-if(params$recount == TRUE & dir.exists(nonSplitCountsDir)){
-  unlink(nonSplitCountsDir, recursive = TRUE)
+nonSplitCountsDir <- file.path(workingDir(fds), "savedObjects", 
+        name(fds), 'nonSplitCounts')
+if(dir.exists(nonSplitCountsDir)){
+  unlink(nonSplitCountsDir, recursive=TRUE)
 }
 
 # Get and merge nonSplitReads for all sample ids
 nonSplitCounts <- getNonSplitReadCountsForAllSamples(fds=fds, 
-                                                     splitCountRanges=splitCounts_gRanges, 
-                                                     minAnchor=5, 
-                                                     recount=FALSE, 
-                                                     longRead=params$longRead)
+        splitCountRanges=splitCounts_gRanges, 
+        minAnchor=5, 
+        recount=FALSE, 
+        longRead=params$longRead)
 
 message(date(), ":", dataset, " nonSplit counts done")
diff --git a/drop/modules/aberrant-splicing-pipeline/Counting/01_5_countRNA_collect.R b/drop/modules/aberrant-splicing-pipeline/Counting/01_5_countRNA_collect.R
index da3d38b6..1af594db 100644
--- a/drop/modules/aberrant-splicing-pipeline/Counting/01_5_countRNA_collect.R
+++ b/drop/modules/aberrant-splicing-pipeline/Counting/01_5_countRNA_collect.R
@@ -4,9 +4,6 @@
 #' wb:
 #'  log:
 #'    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "01_5_collect.Rds")`'
-#'  params:
-#'   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
-#'   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'
 #'  input:
 #'   - countsJ:  '`sm cfg.getProcessedDataDir() + 
 #'                    "/aberrant_splicing/datasets/savedObjects/raw-{dataset}/rawCountsJ.h5"`'
@@ -23,19 +20,23 @@
 #'---
 
 saveRDS(snakemake, snakemake@log$snakemake)
-source(snakemake@params$setup, echo=FALSE)
+suppressPackageStartupMessages(library(FRASER))
 
-dataset    <- snakemake@wildcards$dataset
-workingDir <- snakemake@params$workingDir
+dataset      <- snakemake@wildcards$dataset
+j_counts     <- snakemake@input$countsJ
+theta_counts <- snakemake@input$countsSS
 
+# Force writing HDF5 files
+options(FRASER.maxSamplesNoHDF5=-1)
+options(FRASER.maxJunctionsNoHDF5=-1)
 
 # Read FRASER object
-fds <- loadFraserDataSet(dir=workingDir, name=paste0("raw-", dataset))
+fds <- loadFraserDataSet(file=j_counts)
 splitCounts_gRanges <- readRDS(snakemake@input$gRangesSplitCounts)
 spliceSiteCoords <- readRDS(snakemake@input$spliceSites)
 
 # Get splitReads and nonSplitRead counts in order to store them in FRASER object
-splitCounts_h5 <- HDF5Array::HDF5Array(snakemake@input$countsJ, "rawCountsJ")
+splitCounts_h5 <- HDF5Array::HDF5Array(j_counts, "rawCountsJ")
 splitCounts_se <- SummarizedExperiment(
   colData = colData(fds),
   rowRanges = splitCounts_gRanges,
@@ -43,7 +44,7 @@ splitCounts_se <- SummarizedExperiment(
 )
 
 
-nonSplitCounts_h5 <- HDF5Array::HDF5Array(snakemake@input$countsSS, "rawCountsSS")
+nonSplitCounts_h5 <- HDF5Array::HDF5Array(theta_counts, "rawCountsSS")
 nonSplitCounts_se <- SummarizedExperiment(
   colData = colData(fds),
   rowRanges = spliceSiteCoords,
@@ -51,8 +52,9 @@ nonSplitCounts_se <- SummarizedExperiment(
 )
 
 # Add Counts to FRASER object
-fds <- addCountsToFraserDataSet(fds=fds, splitCounts=splitCounts_se,
-                                nonSplitCounts=nonSplitCounts_se)
+fds <- addCountsToFraserDataSet(fds=fds, 
+    splitCounts=splitCounts_se,
+    nonSplitCounts=nonSplitCounts_se)
 
 # Save final FRASER object 
 fds <- saveFraserDataSet(fds)
diff --git a/drop/modules/aberrant-splicing-pipeline/Counting/02_psi_value_calculation_FraseR.R b/drop/modules/aberrant-splicing-pipeline/Counting/02_psi_value_calculation_FraseR.R
index 24e5cb9b..37e39abc 100644
--- a/drop/modules/aberrant-splicing-pipeline/Counting/02_psi_value_calculation_FraseR.R
+++ b/drop/modules/aberrant-splicing-pipeline/Counting/02_psi_value_calculation_FraseR.R
@@ -4,31 +4,35 @@
 #' wb:
 #'  log:
 #'   - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "02_PSIcalc.Rds")`'
-#'  params:
-#'   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
-#'   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
-#'  threads: 30
+#'  threads: 10
 #'  input:
 #'   - counting_done: '`sm cfg.getProcessedDataDir() + 
 #'                "/aberrant_splicing/datasets/savedObjects/raw-{dataset}/counting.done" `'
 #'  output:
 #'  - theta:     '`sm cfg.getProcessedDataDir() +
-#'                    "/aberrant_splicing/datasets/savedObjects/raw-{dataset}/theta.h5"`'
+#'                    "/aberrant_splicing/datasets/savedObjects/raw-{dataset}/delta_theta.h5"`'
 #'  type: script
 #'--- 
 
 saveRDS(snakemake, snakemake@log$snakemake)
-source(snakemake@params$setup, echo=FALSE)
+suppressPackageStartupMessages(library(FRASER))
 
-dataset    <- snakemake@wildcards$dataset
-workingDir <- snakemake@params$workingDir
-params <- snakemake@config$aberrantSplicing
+# input
+dataset <- snakemake@wildcards$dataset
+fds_in  <- file.path(dirname(snakemake@input$counting_done), "fds-object.RDS")
+params  <- snakemake@config$aberrantSplicing
+BPPARAM  <- MulticoreParam(snakemake@threads)
 
-register(MulticoreParam(snakemake@threads))
-# Limit number of threads for DelayedArray operations
-setAutoBPPARAM(MulticoreParam(snakemake@threads))
+# Set number of threads including for DelayedArray operations
+register(BPPARAM)
+DelayedArray::setAutoBPPARAM(BPPARAM)
 
-fds <- loadFraserDataSet(dir=workingDir, name=paste0("raw-", dataset))
+# Force writing HDF5 files
+options(FRASER.maxSamplesNoHDF5=-1)
+options(FRASER.maxJunctionsNoHDF5=-1)
+
+# load FraserDataSet object
+fds <- loadFraserDataSet(file=fds_in)
 
 # Calculating PSI values
 fds <- calculatePSIValues(fds)
diff --git a/drop/modules/aberrant-splicing-pipeline/Counting/03_filter_expression_FraseR.R b/drop/modules/aberrant-splicing-pipeline/Counting/03_filter_expression_FraseR.R
index 731300ae..3d191b23 100644
--- a/drop/modules/aberrant-splicing-pipeline/Counting/03_filter_expression_FraseR.R
+++ b/drop/modules/aberrant-splicing-pipeline/Counting/03_filter_expression_FraseR.R
@@ -5,53 +5,76 @@
 #'  log:
 #'    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "03_filter.Rds")`'
 #'  params:
-#'   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
-#'   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
+#'   - exCountIDs: '`sm lambda w: sa.getIDsByGroup(w.dataset, assay="SPLICE_COUNT")`'
 #'  input:
 #'   - theta:  '`sm cfg.getProcessedDataDir()+
-#'                  "/aberrant_splicing/datasets/savedObjects/raw-{dataset}/theta.h5"`'
+#'                  "/aberrant_splicing/datasets/savedObjects/raw-{dataset}/delta_theta.h5"`'
+#'   - exCounts: '`sm lambda w: cfg.AS.getExternalCounts(w.dataset, "k_j_counts")`'
 #'  output:
-#'   - fds: '`sm cfg.getProcessedDataDir() +
-#'                "/aberrant_splicing/datasets/savedObjects/{dataset}/fds-object.RDS"`'
-#'   - done: '`sm cfg.getProcessedDataDir() + 
-#'                "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'
+#'   - fds_filter_done: '`sm cfg.getProcessedDataDir() +
+#'                "/aberrant_splicing/datasets/savedObjects/{dataset}/filtering.done"`'
 #'  threads: 3
 #'  type: script
 #'---
 
 saveRDS(snakemake, snakemake@log$snakemake)
-source(snakemake@params$setup, echo=FALSE)
-
-opts_chunk$set(fig.width=12, fig.height=8)
+suppressPackageStartupMessages(library(FRASER))
+knitr::opts_chunk$set(fig.width=12, fig.height=8)
 
 # input
 dataset    <- snakemake@wildcards$dataset
-workingDir <- snakemake@params$workingDir
-params <- snakemake@config$aberrantSplicing
+fdsIn      <- snakemake@input$theta
+fdsOut     <- snakemake@output$fds_filter_done
+params     <- snakemake@config$aberrantSplicing
+exCountIDs <- snakemake@params$exCountIDs
+exCountFiles <- snakemake@input$exCounts
+sample_anno_file <- snakemake@config$sampleAnnotation
+minExpressionInOneSample <- params$minExpressionInOneSample
+minDeltaPsi <- params$minDeltaPsi
+BPPARAM  <- MulticoreParam(snakemake@threads)
 
-fds <- loadFraserDataSet(dir=workingDir, name=paste0("raw-", dataset))
+# Set number of threads including for DelayedArray operations
+register(BPPARAM)
+DelayedArray::setAutoBPPARAM(BPPARAM)
 
-register(MulticoreParam(snakemake@threads))
-# Limit number of threads for DelayedArray operations
-setAutoBPPARAM(MulticoreParam(snakemake@threads))
+# Force writing HDF5 files
+options(FRASER.maxSamplesNoHDF5=-1)
+options(FRASER.maxJunctionsNoHDF5=-1)
 
-# Apply filter
-minExpressionInOneSample <- params$minExpressionInOneSample
-minDeltaPsi <- params$minDeltaPsi
+# Load FraserDataSet object
+fds <- loadFraserDataSet(file=fdsIn)
 
+# Apply filter
 fds <- filterExpressionAndVariability(fds, 
-                        minExpressionInOneSample = minExpressionInOneSample,
-                        minDeltaPsi = minDeltaPsi,
-                        filter=FALSE)
+        minExpressionInOneSample = minExpressionInOneSample,
+        minDeltaPsi = minDeltaPsi,
+        filter=FALSE)
 devNull <- saveFraserDataSet(fds)
 
-# Keep junctions that pass filter
-name(fds) <- dataset
-if (params$filter == TRUE) {
-    filtered <- mcols(fds, type="j")[,"passed"]
-    fds <- fds[filtered,]
-    message(paste("filtered to", nrow(fds), "junctions"))
+# TODO move it before applying filter to have it included in the summary
+# Add external data if provided by dataset
+dontWriteHDF5(fds) <- TRUE
+if(length(exCountIDs) > 0){
+    for(resource in unique(exCountFiles)){
+        exSampleIDs <- exCountIDs[exCountFiles == resource]
+        exAnno <- fread(sample_anno_file, key="RNA_ID")[J(exSampleIDs)]
+        setnames(exAnno, "RNA_ID", "sampleID")
+        
+        ctsNames <- c("k_j", "k_theta", "n_psi3", "n_psi5", "n_theta")
+        ctsFiles <- paste0(dirname(resource), "/", ctsNames, "_counts.tsv.gz")
+        fds <- mergeExternalData(fds=fds, countFiles=ctsFiles,
+                sampleIDs=exSampleIDs, annotation=exAnno)
+    }
 }
 
-fds <- saveFraserDataSet(fds)
-file.create(snakemake@output$done)
+fds <- filterExpressionAndVariability(fds, 
+        minExpressionInOneSample = minExpressionInOneSample,
+        minDeltaPsi = minDeltaPsi,
+        filter=params$filter)
+
+# save filtered data into new dataset object
+dontWriteHDF5(fds) <- FALSE
+name(fds) <- dataset
+fds <- saveFraserDataSet(fds, rewrite=TRUE)
+
+file.create(fdsOut)
\ No newline at end of file
diff --git a/drop/modules/aberrant-splicing-pipeline/Counting/Summary.R b/drop/modules/aberrant-splicing-pipeline/Counting/Summary.R
index e2c61d86..f68fa1e7 100644
--- a/drop/modules/aberrant-splicing-pipeline/Counting/Summary.R
+++ b/drop/modules/aberrant-splicing-pipeline/Counting/Summary.R
@@ -9,7 +9,7 @@
 #'   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
 #'  input:
 #'   - filter: '`sm cfg.getProcessedDataDir() + 
-#'                "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'
+#'                "/aberrant_splicing/datasets/savedObjects/{dataset}/filtering.done"`'
 #'  output:
 #'   - wBhtml: '`sm config["htmlOutputPath"] + 
 #'                  "/AberrantSplicing/{dataset}_countSummary.html"`'
diff --git a/drop/modules/aberrant-splicing-pipeline/FRASER/04_fit_hyperparameters_FraseR.R b/drop/modules/aberrant-splicing-pipeline/FRASER/04_fit_hyperparameters_FraseR.R
index 1a99b259..b2db290d 100644
--- a/drop/modules/aberrant-splicing-pipeline/FRASER/04_fit_hyperparameters_FraseR.R
+++ b/drop/modules/aberrant-splicing-pipeline/FRASER/04_fit_hyperparameters_FraseR.R
@@ -4,13 +4,10 @@
 #' wb:
 #'  log:
 #'    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "04_hyper.Rds")`'
-#'  params:
-#'   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
-#'   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
 #'  threads: 12
 #'  input:
 #'   - filter: '`sm cfg.getProcessedDataDir() + 
-#'                "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'
+#'                "/aberrant_splicing/datasets/savedObjects/{dataset}/filtering.done"`'
 #'  output:
 #'   - hyper: '`sm cfg.getProcessedDataDir() + 
 #'                "/aberrant_splicing/datasets/savedObjects/{dataset}/hyper.done" `'
@@ -18,7 +15,10 @@
 #'---
 
 saveRDS(snakemake, snakemake@log$snakemake)
-source(snakemake@params$setup, echo=FALSE)
+suppressPackageStartupMessages({
+  library(FRASER)
+  library(tidyr)
+})
 
 if ("random_seed" %in% names(snakemake@config)){
   rseed <- snakemake@config$random_seed
@@ -30,15 +30,20 @@ if ("random_seed" %in% names(snakemake@config)){
 }
 
 #+ input
-dataset    <- snakemake@wildcards$dataset
-workingDir <- snakemake@params$workingDir
+dataset  <- snakemake@wildcards$dataset
+fds_file <- file.path(dirname(snakemake@input$filter), "fds-object.RDS")
+BPPARAM  <- MulticoreParam(snakemake@threads)
 
-register(MulticoreParam(snakemake@threads))
-# Limit number of threads for DelayedArray operations
-setAutoBPPARAM(MulticoreParam(snakemake@threads))
+# Set number of threads including for DelayedArray operations
+register(BPPARAM)
+DelayedArray::setAutoBPPARAM(BPPARAM)
+
+# Force writing HDF5 files
+options(FRASER.maxSamplesNoHDF5=-1)
+options(FRASER.maxJunctionsNoHDF5=-1)
 
 # Load PSI data
-fds <- loadFraserDataSet(dir=workingDir, name=dataset)
+fds <- loadFraserDataSet(file=fds_file)
 
 # Run hyper parameter optimization
 implementation <- snakemake@config$aberrantSplicing$implementation
diff --git a/drop/modules/aberrant-splicing-pipeline/FRASER/05_fit_autoencoder_FraseR.R b/drop/modules/aberrant-splicing-pipeline/FRASER/05_fit_autoencoder_FraseR.R
index f5e760c8..e87cf310 100644
--- a/drop/modules/aberrant-splicing-pipeline/FRASER/05_fit_autoencoder_FraseR.R
+++ b/drop/modules/aberrant-splicing-pipeline/FRASER/05_fit_autoencoder_FraseR.R
@@ -4,9 +4,6 @@
 #' wb:
 #'  log:
 #'    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "05_fit.Rds")`'
-#'  params:
-#'   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
-#'   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
 #'  threads: 20
 #'  input:
 #'   - hyper: '`sm cfg.getProcessedDataDir() + 
@@ -18,16 +15,23 @@
 #'---
 
 saveRDS(snakemake, snakemake@log$snakemake)
-source(snakemake@params$setup, echo=FALSE)
+suppressPackageStartupMessages(library(FRASER))
 
-dataset    <- snakemake@wildcards$dataset
-workingDir <- snakemake@params$workingDir
+# input
+dataset <- snakemake@wildcards$dataset
+fds_in  <- file.path(dirname(snakemake@input$hyper), "fds-object.RDS")
+BPPARAM <- MulticoreParam(snakemake@threads)
 
-register(MulticoreParam(snakemake@threads))
-# Limit number of threads for DelayedArray operations
-setAutoBPPARAM(MulticoreParam(snakemake@threads))
+# Set number of threads including for DelayedArray operations
+register(BPPARAM)
+DelayedArray::setAutoBPPARAM(BPPARAM)
 
-fds <- loadFraserDataSet(dir=workingDir, name=dataset)
+# Force writing HDF5 files
+options(FRASER.maxSamplesNoHDF5=-1)
+options(FRASER.maxJunctionsNoHDF5=-1)
+
+# load FraserDataSet object
+fds <- loadFraserDataSet(file=fds_in)
 
 # Fit autoencoder
 # run it for every type
diff --git a/drop/modules/aberrant-splicing-pipeline/FRASER/06_calculation_stats_AE_FraseR.R b/drop/modules/aberrant-splicing-pipeline/FRASER/06_calculation_stats_AE_FraseR.R
index 84b222cb..c2caf9fb 100644
--- a/drop/modules/aberrant-splicing-pipeline/FRASER/06_calculation_stats_AE_FraseR.R
+++ b/drop/modules/aberrant-splicing-pipeline/FRASER/06_calculation_stats_AE_FraseR.R
@@ -4,9 +4,6 @@
 #' wb:
 #'  log:
 #'    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "06_stats.Rds")`'
-#'  params:
-#'   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
-#'   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
 #'  threads: 20
 #'  input:
 #'   - fdsin:  '`sm cfg.getProcessedDataDir() + 
@@ -20,18 +17,23 @@
 #'---
 
 saveRDS(snakemake, snakemake@log$snakemake)
-source(snakemake@params$setup, echo=FALSE)
+suppressPackageStartupMessages(library(FRASER))
 
-dataset    <- snakemake@wildcards$dataset
-fdsFile    <- snakemake@input$fdsin
-workingDir <- snakemake@params$workingDir
+#+ input
+dataset  <- snakemake@wildcards$dataset
+fdsFile  <- snakemake@input$fdsin
+BPPARAM  <- MulticoreParam(snakemake@threads)
 
-register(MulticoreParam(snakemake@threads))
-# Limit number of threads for DelayedArray operations
-setAutoBPPARAM(MulticoreParam(snakemake@threads))
+# Set number of threads including for DelayedArray operations
+register(BPPARAM)
+DelayedArray::setAutoBPPARAM(BPPARAM)
+
+# Force writing HDF5 files
+options(FRASER.maxSamplesNoHDF5=-1)
+options(FRASER.maxJunctionsNoHDF5=-1)
 
 # Load Zscores data
-fds <- loadFraserDataSet(dir=workingDir, name=dataset)
+fds <- loadFraserDataSet(file=fdsFile)
 
 # Calculate stats
 for (type in psiTypes) {
diff --git a/drop/modules/aberrant-splicing-pipeline/FRASER/07_extract_results_FraseR.R b/drop/modules/aberrant-splicing-pipeline/FRASER/07_extract_results_FraseR.R
index dce06ba0..dca8bdb5 100644
--- a/drop/modules/aberrant-splicing-pipeline/FRASER/07_extract_results_FraseR.R
+++ b/drop/modules/aberrant-splicing-pipeline/FRASER/07_extract_results_FraseR.R
@@ -14,7 +14,6 @@
 #'   - assemblyVersion: '`sm cfg.genome.getBSGenomeVersion()`'
 #'  threads: 10
 #'  input:
-#'   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
 #'   - add_HPO_cols: '`sm str(projectDir / ".drop" / "helpers" / "add_HPO_cols.R")`'
 #'   - fdsin: '`sm cfg.getProcessedDataDir() +
 #'                 "/aberrant_splicing/datasets/savedObjects/{dataset}/" +
@@ -32,22 +31,33 @@
 #'---
 
 saveRDS(snakemake, snakemake@log$snakemake)
-source(snakemake@input$setup, echo=FALSE)
+suppressPackageStartupMessages({
+  library(FRASER)
+  library(tidyr)
+  library(AnnotationDbi)
+})
 source(snakemake@input$add_HPO_cols)
-library(AnnotationDbi)
+knitr::opts_chunk$set(fig.width=12, fig.height=8)
 
-opts_chunk$set(fig.width=12, fig.height=8)
-
-annotation    <- snakemake@wildcards$annotation
+# input
 dataset    <- snakemake@wildcards$dataset
 fdsFile    <- snakemake@input$fdsin
+BPPARAM    <- MulticoreParam(snakemake@threads)
+annotation <- snakemake@wildcards$annotation
 workingDir <- snakemake@params$workingDir
 outputDir  <- snakemake@params$outputDir
 assemblyVersion <- snakemake@params$assemblyVersion
+outResJunc <- snakemake@output$resultTableJunc
+outResGene <- snakemake@output$resultTableGene
+
+# Set number of threads including for DelayedArray operations
+register(BPPARAM)
+DelayedArray::setAutoBPPARAM(BPPARAM)
+
+# Force writing HDF5 files
+options(FRASER.maxSamplesNoHDF5=-1)
+options(FRASER.maxJunctionsNoHDF5=-1)
 
-register(MulticoreParam(snakemake@threads))
-# Limit number of threads for DelayedArray operations
-setAutoBPPARAM(MulticoreParam(snakemake@threads))
 
 # Load fds and create a new one
 fds_input <- loadFraserDataSet(dir=workingDir, name=dataset)
@@ -106,5 +116,5 @@ if(length(res_junc) > 0){
 } else res_genes_dt <- data.table()
 
 # Results
-write_tsv(res_junc_dt, file=snakemake@output$resultTableJunc)
-write_tsv(res_genes_dt, file=snakemake@output$resultTableGene)
+write.table(x=res_junc_dt,  file=outResJunc, quote=FALSE, sep='\t', row.names=FALSE)
+write.table(x=res_genes_dt, file=outResGene, quote=FALSE, sep='\t', row.names=FALSE)
diff --git a/drop/modules/aberrant-splicing-pipeline/FRASER/Summary.R b/drop/modules/aberrant-splicing-pipeline/FRASER/Summary.R
index a24168a5..d8b549c9 100644
--- a/drop/modules/aberrant-splicing-pipeline/FRASER/Summary.R
+++ b/drop/modules/aberrant-splicing-pipeline/FRASER/Summary.R
@@ -62,7 +62,7 @@ topN <- 30000
 topJ <- 10000
 for(type in psiTypes){
   before <- plotCountCorHeatmap(
-    fds,
+    object=fds,
     type = type,
     logit = TRUE,
     topN = topN,
@@ -78,7 +78,7 @@ for(type in psiTypes){
   )
   before
   after <- plotCountCorHeatmap(
-    fds,
+    object=fds,
     type = type,
     logit = TRUE,
     topN = topN,
diff --git a/drop/requirementsR.txt b/drop/requirementsR.txt
index 02151c2d..b6fb8718 100644
--- a/drop/requirementsR.txt
+++ b/drop/requirementsR.txt
@@ -1,6 +1,6 @@
 package	version
 gagneurlab/OUTRIDER	1.6.1
-c-mertes/FRASER	1.2.1
+c-mertes/FRASER	1.2.2
 mumichae/tMAE	1.0.0
 VariantAnnotation	
 rmarkdown	
diff --git a/drop/utils.py b/drop/utils.py
index b325f38f..975c80b6 100644
--- a/drop/utils.py
+++ b/drop/utils.py
@@ -76,11 +76,20 @@ def subsetBy(df, column, values, exact_match=True):
     """
     if values is None:
         return df
-    elif isinstance(values, str) and exact_match :
-        return df[df[column] == values]
-    elif not isinstance(values,str) and exact_match:
-        return df[df[column].isin(values)]
-    elif isinstance(values,str) and not exact_match:
+#    elif isinstance(values, str):
+#        return df[df[column].str.contains("(^|,)" + values + "(,|$)")]
+#    else:
+#        if(values.__len__() > 1):
+#            raise ValueError(f"Values too long! Please report this. Values are: {values}.")
+    elif exact_match:
+        if isinstance(values, str):
+            return df[df[column] == values]
+        else:
+            return df[df[column].isin(values)]
+    elif isinstance(values,str):
         return df[df[column].str.contains(values)]
     else:
+        # this does not work. If you have a group drop and drop_2 
+        # first group will match the second. Also if you have drop,drop_2 
+        # it will not detect on or the other. 
         return df[df[column].str.contains("|".join(values))]
diff --git a/tests/config/test_AE.py b/tests/config/test_AE.py
index fa1e1023..8643130d 100644
--- a/tests/config/test_AE.py
+++ b/tests/config/test_AE.py
@@ -35,7 +35,7 @@ def test_getCountsFiles(self, demo_dir, dropConfig):
 
         # import count
         counts_files_true = counts_files_true[2:]
-        counts_files_true.append(f"{demo_dir}/Data/external_geneCounts.tsv.gz")
+        counts_files_true.append(f"{demo_dir}/Data/external_count_data/geneCounts.tsv.gz")
         counts_files_true.sort()
         counts_files_test = dropConfig.AE.getCountFiles(annotation="v29", group="import_exp")
         counts_files_test.sort()
diff --git a/tests/config/test_AS.py b/tests/config/test_AS.py
index df6b527d..c3e3dc38 100644
--- a/tests/config/test_AS.py
+++ b/tests/config/test_AS.py
@@ -3,7 +3,7 @@ class Test_AS_Config:
     def test_config(self, dropConfig,demo_dir):
         assert dropConfig.AS.getWorkdir() == f"{demo_dir}/Scripts/AberrantSplicing/pipeline"
         dict_ = {
-            'groups': ['fraser'],
+            'groups': ['fraser', 'fraser_ex'],
             'recount': True,
             'longRead': False,
             'keepNonStandardChrs': True,
diff --git a/tests/config/test_SampleAnnotation.py b/tests/config/test_SampleAnnotation.py
index ba93966f..f1e1d21e 100644
--- a/tests/config/test_SampleAnnotation.py
+++ b/tests/config/test_SampleAnnotation.py
@@ -13,9 +13,9 @@ def test_columns(self, sampleAnnotation):
 
     def test_mapping(self, sampleAnnotation):
         # ID mappings/groups
-        assert sampleAnnotation.idMapping.shape == (22, 2)
-        assert sampleAnnotation.sampleFileMapping.shape == (32, 4)
-        true_mapping = {'mae': 2, 'import_exp': 8, 'outrider': 10, 'fraser': 10}
+        assert sampleAnnotation.idMapping.shape == (24, 2)
+        assert sampleAnnotation.sampleFileMapping.shape == (35, 4)
+        true_mapping = {'mae': 2, 'import_exp': 8, 'outrider': 10, 'fraser': 10, 'fraser_ex': 10}
         assert true_mapping == {k: len(v) for k, v in sampleAnnotation.rnaIDs.items()}
         assert true_mapping == {k: len(v) for k, v in sampleAnnotation.dnaIDs.items()}
 
@@ -23,8 +23,9 @@ def test_mapping(self, sampleAnnotation):
         "sample_id,file_type,file_name",
         [
             ("HG00096.1.M_111124_6", "RNA_BAM_FILE", "Data/rna_bam/HG00096.1.M_111124_6_chr21.bam"),
-            ("HG00178.4.M_120208_8", "GENE_COUNTS_FILE", "Data/external_geneCounts.tsv.gz"),
-            ("HG00096", "DNA_VCF_FILE", "Data/dna_vcf/demo_chr21.vcf.gz")
+            ("HG00178.4.M_120208_8", "GENE_COUNTS_FILE", "Data/external_count_data/geneCounts.tsv.gz"),
+            ("HG00096", "DNA_VCF_FILE", "Data/dna_vcf/demo_chr21.vcf.gz"),
+            ("HG00201.1.M_120208_6", "SPLICE_COUNTS_DIR", "Data/external_count_data")
         ]
     )
     def test_filePaths(self, demo_dir, sampleAnnotation, sample_id, file_type, file_name):
@@ -35,7 +36,7 @@ def test_filePaths(self, demo_dir, sampleAnnotation, sample_id, file_type, file_
     @pytest.mark.parametrize(
         "annotation,group,files",
         [
-            ("v29", "import_exp", {'Data/external_geneCounts.tsv.gz'})
+            ("v29", "import_exp", {'Data/external_count_data/geneCounts.tsv.gz'})
         ]
     )
     def test_import(self, demo_dir, sampleAnnotation, annotation, group, files):