Using the HPC to run jobs in parallel

Type:

cat > chick-tophat-3.sh <<EOF

and then paste this in:

#PBS -l walltime=24:00:00,nodes=1:ppn=2,mem=10gb
module load TopHat2/2.0.12
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_male_repl1 \
    ~/RNAseq-semimodel/reference/Gallus_gallus/UCSC/galGal3/Sequence/Bowtie2Index/genome \
    male_repl1_R1.qc.fq.gz male_repl1_R2.qc.fq.gz

htseq-count --format=bam --stranded=no --order=pos \
    tophat_male_repl1/accepted_hits.bam \
    cuffmerge_all/nostrand.gtf > male_repl1_counts.txt

EOF

Next, do it for male_repl2:

cat > chick-tophat-4.sh <<EOF

and then paste this in:

#PBS -l walltime=24:00:00,nodes=1:ppn=2,mem=10gb
module load TopHat2/2.0.12
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_male_repl2 \
    ~/RNAseq-semimodel/reference/Gallus_gallus/UCSC/galGal3/Sequence/Bowtie2Index/genome \
    male_repl2_R1.qc.fq.gz male_repl2_R2.qc.fq.gz

htseq-count --format=bam --stranded=no --order=pos \
    tophat_male_repl2/accepted_hits.bam \
    cuffmerge_all/nostrand.gtf > male_repl2_counts.txt

EOF

To submit these to the queue, do:

qsub chick-tophat-3.sh
qsub chick-tophat-4.sh

And now wait until they’re done; you can figure that out by doing:

qstat -u $USER

to monitor the status of the job; once it goes away, it will be done.

Next: Data analysis & differential expression

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