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wiki:simple_pipeline_3
#!/usr/bin/env bash
 
#SBATCH --job-name=pipeline_demo 
#SBATCH --nodes=1
#SBATCH --ntasks=6      # modify this number to reflect how many cores you want to use (up to 24)
#SBATCH --partition=shas-testing
#SBATCH --qos=testing     # modify this to reflect which queue you want to use. Options are 'normal' and 'testing'
#SBATCH --time=0:29:00   # modify this to reflect how long to let the job go. 
#SBATCH --output=log_pipeline_demo_%j.txt
 
# Source the bashrc link to install software
source /scratch/summit/<eID>@colostate.edu/activate.bashrc
 
# Quality control with FASTQC
#fastqc -t 6 -o ../03_output ../01_input/SRR3567551_1.fastq
#fastqc -t 6 -o ../03_output ../01_input/SRR3567551_2.fastq
 
 
# Alignment to reference genome with hisat2
#hisat2 --summary-file ../03_output/sample01_summary.txt --no-unal -p 6 -x /scratch/summit/erinnish@colostate.edu/DSCI512_RNAseq/PROJ02_yeastGenome/by_chrom/sc3 -1 ../01_input/SRR3567551_1.fastq -2 ../01_input/SRR3567551_2.fastq -S ../03_output/sample01.sam
 
# Tabulation of read counts per gene with featureCounts
featureCounts -p -Q 20 -T 6 -a /scratch/summit/<eID>@colostate.edu/DSCI512_RNAseq/PROJ02_yeastGenome/181115_Scer_annotation.gtf.gz -o ../03_output/feature_counts.txt ../03_output/sample01.sam

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wiki/simple_pipeline_3.txt · Last modified: 2018/11/22 13:29 by erin