Processing another sample with TopHat and HTSeqΒΆ

Let’s script this!


cd ~/rnaseq/
cat > <<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


(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:


This will run all of the commands in the file ‘’.

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


Next: Using the HPC to run jobs in parallel

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