2021-02-25 12:40:17 +01:00
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#!/bin/bash
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PROJECT_DIRECTORY="/groups/umcg-griac/tmp01/rawdata/$(whoami)/rnaseq"
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COUNT_OUTPUT="${PROJECT_DIRECTORY}/step5"
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mkdir -p "${COUNT_OUTPUT}"
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# Storage location of annotation on Gearshift.
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REFERENCE_DATA="/groups/umcg-griac/prm03/rawdata/reference/genome"
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GTF_FILE="${REFERENCE_DATA}/Homo_sapiens.GRCh38.100.gtf"
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# Where our alignment file was stored.
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BAM="${PROJECT_DIRECTORY}/step3/alignment/sample1_Aligned.sortedByCoord.out.bam"
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# Compute counts using htseq-count.
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#
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# N.B.:
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# - If you are processing multiple files, you can use the --nprocesses flag to
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# compute the files in parallel.
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htseq-count \
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${BAM} \
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${GTF_FILE} \
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> ${COUNT_OUTPUT}/counts.txt
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