slurm-submit-script-WITHOUT-containers.sh
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slurm-submit-script-WITHOUT-containers.sh
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			#!/bin/bash

			#SBATCH --job-name=all-steps
			#SBATCH --partition=shi # partition
			#SBATCH --time=02:00:00 # Walltime
			#SBATCH --cpus-per-task=8
			#SBATCH --mem=48G
			#SBATCH --workdir=/scicore/home/scicore/escobar/Containers-pipeline
			#SBATCH --output=logs/all-steps.log

			module load STAR/2.5.2a-goolf-1.7.20
			module load HTSeq/0.6.1p1-goolf-1.7.20-Python-2.7.11
			module load Pysam/0.9.0-goolf-1.7.20-Python-2.7.11

			STAR --runThreadN ${SLURM_CPUS_PER_TASK} --outTmpDir $TMPDIR/star_tmp --runMode genomeGenerate --genomeDir ./GRCm38_Genome --genomeFastaFiles ./GRCm38_Genome/Ensembl_GRCm38.fa --sjdbGTFfile ./GRCm38_Genome/Ensembl_GRCm38_genes.gtf

			STAR --runThreadN ${SLURM_CPUS_PER_TASK} --outTmpDir $TMPDIR/star_tmp --readFilesCommand zcat --genomeDir GRCm38_Genome/ --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFileNamePrefix TAM3_ --readFilesIn ./fastq/SRR3180540_pass_1.fastq.gz

			htseq-count -f bam -r pos -s no TAM3_Aligned.sortedByCoord.out.bam GRCm38_Genome/Ensembl_GRCm38_genes.gtf > TAM3.counts