Processing another sample with TopHat and HTSeq

Let’s script this!

Type:

cd ~/rnaseq/
cat > chick-tophat-2.sh <<EOF

and then paste this in:

module load TopHat2/2.0.12
module load PySAM/0.6
module load HTSeq/0.6.1

# go to the 'rnaseq' directory in my home directory
cd ~/rnaseq

# now run Tophat!
tophat \
    -G cuffmerge_all/nostrand.gtf \
    --transcriptome-index=\$HOME/RNAseq-semimodel/tophat/merged \
    -o tophat_female_repl2 \
    ~/RNAseq-semimodel/reference/Gallus_gallus/UCSC/galGal3/Sequence/Bowtie2Index/genome \
    female_repl2_R1.qc.fq.gz female_repl2_R2.qc.fq.gz

htseq-count --format=bam --stranded=no --order=pos \
    tophat_female_repl2/accepted_hits.bam \
    cuffmerge_all/nostrand.gtf > female_repl2_counts.txt

EOF

(Be sure to press the Enter or Return key after pasting this in!) This is called a ‘heredoc’ and it gives a way to write a shell script via copy-paste ;).

Next, type:

bash chick-tophat-2.sh

This will run all of the commands in the file ‘chick-tophat-2.sh’.

You can use the ‘nano’ editor to modify this file – type:

nano chick-tophat-2.sh

Next: Using the HPC to run jobs in parallel

---

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.

---