Setting up more scripts

(If you’re using an HPC or multiple computers, you can run these in parallel; here, we’ll just run them one at a time.)

Type:

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

and then paste this in:

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

# now run Tophat!
tophat \
    -G cuffmerge_all/nostrand.gtf \
    --transcriptome-index=/mnt/genome/tophat/merged \
    -o tophat_male_repl1 \
    /mnt/genome/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:

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

# now run Tophat!
tophat \
    -G cuffmerge_all/nostrand.gtf \
    --transcriptome-index=/mnt/genome/tophat/merged \
    -o tophat_male_repl2 \
    /mnt/genome/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

and then run them with:

bash chick-tophat-3.sh
bash chick-tophat-4.sh

Next: Data analysis & differential expression

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