rnaseqpipe.sh

#!/usr/bin/bash
#Author: Vijay Nagarajan
#Description: this is a pipeline for primary rnaseq analysis

#letting shell know where the programs are
source /etc/profile.d/markcbm.sh

#data prep
cp -R /home/manager/linux Desktop/.
cd ~/Desktop/linux/advanced/rnaseq/

#step1 fastqc analysis
fastqc fastq/*.fastq

#step 2 building index
cd index
bowtie-build mm9_chr1.fa mm9_chr1
cd ..

#step 3 alignment
tophat2 -G mm9_chr1.gtf -o tophat_wt/ index/mm9_chr1 fastq/myoblast_wt.fastq
tophat2 -G mm9_chr1.gtf -o tophat_del/ index/mm9_chr1 fastq/myoblast_del.fastq

#step 4 check outputs
ls
ls tophat_wt/
ls tophat_del/
cat tophat_wt/align_summary.txt
cat tophat_del/align_summary.txt

#bam indexing
samtools19 index tophat_wt/accepted_hits.bam
samtools19 index tophat_del/accepted_hits.bam

#differential expression analysis
cuffdiff --no-update-check -o cuffdiff_out -L wt,del mm9_chr1.gtf tophat_wt/accepted_hits.bam tophat_del/accepted_hits.bam

ls -lh cuffdiff_out

echo "The RNA-Seq Pipeline is complete"