Examples
Case 1: Unstranded, Paired-end, Mouse Case 2: Stranded, Paired-end, Mouse Case 3: Unstranded, Single-end, Mouse Case 4: Stranded, Single-end, Mouse Case 5: Unstranded, Paired-end, Human Case 6: Stranded, Paired-end, Human Case 7: Unstranded, Single-end, Human Case 8: Stranded, Single-end, Human
Case 1: Unstranded, Paired-end, Mouse nextflow run rikenbit/ramdaq -profile docker \
--genome GRCm39_vM26 --local_annot_dir < path to annotation> \
--reads ' *_{R1,R2}_001.fastq.gz' < path to outdir> Case 2: Stranded, Paired-end, Mouse nextflow run rikenbit/ramdaq -profile docker \
--genome GRCm39_vM26 --local_annot_dir < path to annotation> \
--stranded fr-firststrand \
--reads ' *_{R1,R2}_001.fastq.gz' < path to outdir> Case 3: Unstranded, Single-end, Mouse nextflow run rikenbit/ramdaq -profile docker \
--genome GRCm39_vM26 --local_annot_dir < path to annotation> \
--single_end \
--reads ' *_{R1}_001.fastq.gz' < path to outdir> Case 4: Stranded, Single-end, Mouse nextflow run rikenbit/ramdaq -profile docker
--genome GRCm39_vM26 --local_annot_dir < path to annotation> \
--stranded fr-firststrand --single_end \
--reads ' *_{R1}_001.fastq.gz' < path to outdir> Case 5: Unstranded, Paired-end, Human nextflow run rikenbit/ramdaq -profile docker \
--genome GRCh38_v37 --local_annot_dir < path to annotation> ＼
--reads ' *_{R1,R2}_001.fastq.gz' < path to outdir> Case 6: Stranded, Paired-end, Human nextflow run rikenbit/ramdaq -profile docker \
--genome GRCh38_v37 --local_annot_dir < path to annotation> \
--stranded fr-firststrand \
--reads ' *_{R1,R2}_001.fastq.gz' < path to outdir> Case 7: Unstranded, Single-end, Human nextflow run rikenbit/ramdaq -profile docker \
--genome GRCh38_v37 --local_annot_dir < path to annotation> \
--single_end \
--reads ' *_{R1}_001.fastq.gz' < path to outdir> Case 8: Stranded, Single-end, Human nextflow run rikenbit/ramdaq -profile docker \
--genome GRCh38_v37 --local_annot_dir < path to annotation> \
--stranded fr-firststrand --single_end \
--reads ' *_{R1}_001.fastq.gz' < path to outdir>