STAT555-Project/countdata.sh at master · barbolute/STAT555-Project · GitHub

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# Stop this script on any error.
set -euo pipefail

# The gene feature file
GTFSRR=srr/SRR.gff
GTFLRR=lrr/LRR.gff

# Collect the output of commands here.
RUNLOG=runlog.txt

echo "*** Counting features with: $GTFSRR"
featureCounts -T 14 -a $GTFSRR -g gene_name -o LRR_Cuffcounts.txt  bam/LRR_C*.bam  bam/LRR_T*.bam 2>> $RUNLOG

featureCounts -T 16 -a merged.gtf -g gene_id -o mergedcounts.txt SRR/bam/SRR_*.bam LRR/bam/LRR_*.bam


#simple counts
cat LRR_Cuffcounts.txt | cut -f 1,7-12 > simpleLRR_Cuffcounts.txt


echo "*** Generating simple counts."
cat counts.txt | cut -f 1,7-12 > simple_counts.txt

echo "*** Running DESeq1."
curl -s -O http://data.biostarhandbook.com/rnaseq/code/deseq1.r
cat simple_counts.txt | Rscript deseq1.r 3x3 > results_deseq1.txt  2>> $RUNLOG

echo "*** Running DESeq2."
curl -s -O http://data.biostarhandbook.com/rnaseq/code/deseq2.r
cat simple_counts.txt | Rscript deseq2.r 3x3 > results_deseq2.txt  2>> $RUNLOG

echo "*** Running EdgeR."
curl -s -O http://data.biostarhandbook.com/rnaseq/code/edger.r
cat simple_counts.txt | Rscript edger.r 3x3 > results_edger.txt  2>> $RUNLOG