update blacklist beds, archive, add docs for new lists, change paths …

…for hs1
CCBR · Sep 22, 2023 · 794bd41 · 794bd41
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commit 794bd41
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diff --git a/.test/config_lint.yaml b/.test/config_lint.yaml
@@ -128,7 +128,7 @@ reference:
   hs1:
     fa: "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs1/hs1.fa"
     gtf: "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs1/genes.gtf"
-    blacklist: "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs1/T2T.excluderanges.bed"
+    blacklist: "PIPELINE_HOME/resources/blacklistbed/hs1.bed"
     tss_bed: "PIPELINE_HOME/resources/tss_bed/hs1.tss.bed"
     regions: "chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY"
     macs2_g: "3.1e+8"

diff --git a/config/config.yaml b/config/config.yaml
@@ -128,7 +128,7 @@ reference:
   hs1:
     fa: "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs1/hs1.fa"
     gtf: "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs1/genes.gtf"
-    blacklist: "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs1/T2T.excluderanges.bed"
+    blacklist: "PIPELINE_HOME/resources/blacklistbed/hs1.bed"
     tss_bed: "PIPELINE_HOME/resources/tss_bed/hs1.tss.bed"
     regions: "chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY"
     macs2_g: "3.1e+8"

diff --git a/resources/blacklistbed/README.md b/resources/blacklistbed/README.md
@@ -1,5 +1,15 @@
-# hg38 blacklist
-source location: /data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/indexes/hg38.blacklist.v3.fa
+# current blacklist
+## developed from https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03027-3#MOESM2
+## data location in Additional file 2
+### hg38
+### mm10
+### hs1 (t2t)
+
+## hg19
+source location: /data/khanlab3/gb_omics/processed_DATA/YueHu/cutrun_120822/hg19_blacklist.bed
 
-# hg19 blacklist
-source location: /data/khanlab3/gb_omics/processed_DATA/YueHu/cutrun_120822/hg19_blacklist.bed
+# Retiring blacklists below: 9/22/23
+## hg38 blacklist
+source location: /data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/indexes/hg38.blacklist.v3.fa
+## t2t blacklist
+source location: /data/CCBR_Pipeliner/db/PipeDB/Indices/hs1/T2T.excluderanges.bed