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R2915/SIS/scicore_pipeline1_LSF/LSF_submit-script-with-containers.sh
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LSF_submit-script-with-containers.sh
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#!/bin/bash
#BSUB -J scicore_pipeline1_with_containers
#BSUB -W 02:00:00
#BSUB -n 4
#BSUB -R "[mem=2048]"
#BSUB -R beta
#BSUB -R singularity
#BSUB -o scicore_pipeline1_with_containers.out
#BSUB -e scicore_pipeline1_with_containers.err
# create output directories if they do not exist
[ -d output/STAR ] || mkdir -p output/STAR
[ -d output/htseq-count ] || mkdir -p output/htseq-count
# step 1. Index the reference genome using the STAR utility
singularity exec pipeline1.img STAR --runThreadN 4 --outTmpDir $TMPDIR/star_tmp --runMode genomeGenerate \
--genomeDir ./scicore-pipeline1-input-data/GRCm38_Genome --genomeFastaFiles ./scicore-pipeline1-input-data/GRCm38_Genome/Ensembl_GRCm38.fa \
--sjdbGTFfile ./scicore-pipeline1-input-data/GRCm38_Genome/Ensembl_GRCm38_genes.gtf --outFileNamePrefix=output/STAR/
# step 2. Align reads from fastq to indexed reference genome using STAR utility
singularity exec pipeline1.img STAR --runThreadN 4 --outTmpDir $TMPDIR/star_tmp --readFilesCommand zcat \
--genomeDir ./scicore-pipeline1-input-data/GRCm38_Genome --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate \
--outReadsUnmapped Fastx --outFileNamePrefix output/STAR/TAM3_ --readFilesIn ./scicore-pipeline1-input-data/fastq/SRR3180540_pass_1.fastq.gz
# step 3. Summarize alignment BAM file to counts table by gene feature using HTSeq utility
singularity exec pipeline1.img htseq-count -f bam -r pos -s no output/STAR/TAM3_Aligned.sortedByCoord.out.bam \
./scicore-pipeline1-input-data/GRCm38_Genome/Ensembl_GRCm38_genes.gtf > output/htseq-count/TAM3.counts
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