29 lines
1022 B
Bash
29 lines
1022 B
Bash
#!/bin/bash
|
|
PROJECT_DIRECTORY="/groups/umcg-griac/tmp01/rawdata/$(whoami)/rnaseq"
|
|
COUNT_OUTPUT="${PROJECT_DIRECTORY}/step5"
|
|
mkdir -p "${COUNT_OUTPUT}"
|
|
|
|
# Storage location of annotation on Gearshift.
|
|
REFERENCE_DATA="/groups/umcg-griac/prm03/rawdata/reference/genome"
|
|
GTF_FILE="${REFERENCE_DATA}/Homo_sapiens.GRCh38.100.gtf"
|
|
|
|
# Where our alignment file was stored.
|
|
BAM="${PROJECT_DIRECTORY}/step3/alignment/sample1_Aligned.sortedByCoord.out.bam"
|
|
|
|
# Compute counts using htseq-count.
|
|
#
|
|
# N.B.:
|
|
# - If you are processing multiple files, consider using the `--nprocesses` flag
|
|
# to distribute computation of the files to different cores.
|
|
# - The BAM file must be position sorted. If you used STAR with the
|
|
# `SortedByCoordinate` option you should be okay. If not, sort your BAM file
|
|
# using `samtools sort`.
|
|
# - By default, strand aware library preparation is assumed. If not, specify the
|
|
# `--stranded` flag.
|
|
htseq-count \
|
|
--order pos \
|
|
-f bam \
|
|
${BAM} \
|
|
${GTF_FILE} \
|
|
> ${COUNT_OUTPUT}/counts.txt
|