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#PBS -l nodes=1:ppn=4
# link in the data from the shared folder, no need to copy, just symlink with ln -s
ln -s /srv/projects/db/GEN220/RNAseq/yeast_15hrs_fermentation.fastq .
ln -s /srv/projects/db/GEN220/RNAseq/yeast_1hr_fermentation.fastq .
module load tophat/2.0.5
module load cufflinks/2.0.2
module load bowtie2
#Let's locate all the genome files in this genome directory
if [ ! -d genome ]; then
git clone git://
# uncompress the genome file which came from
# convert the chromsome names to chrI, chrII from ref|NC_XXXX
tar zxf /srv/projects/db/GEN220/S288C_reference_genome_R64-1-1_20110203.tgz
perl htbda_perl_class/examples/NGS/ S288C_reference_genome_R64-1-1_20110203/S288C_reference_sequence_R64-1-1_20110203.fsa > Saccharomyces.fa
# extract the first 16425 lines of the GFF file so the sequence that is appended at the end can be ignore
head -n 16425 S288C_reference_genome_R64-1-1_20110203/saccharomyces_cerevisiae_R64-1-1_20110208.gff > saccharomyces_cerevisiae_R64-1-1_20110208.noseq.gff
mkdir -p genome
mv Saccharomyces.fa genome
cp saccharomyces_cerevisiae_R64-1-1_20110208.noseq.gff genome/Saccharomyces.gff
bowtie2-build genome/Saccharomyces.fa genome/Saccharomyces
# -I max intron length in saccharomyces is ~300 bp - for animals this would be much bigger
if [ ! -f tophat_yeast1hr/accepted_hits.bam ]; then
tophat -p 4 -I 500 -G genome/Saccharomyces.gff -o tophat_yeast1hr genome/Saccharomyces yeast_1hr_fermentation.fastq
if [ ! -f tophat_yeast15hr/accepted_hits.bam ]; then
tophat -p 4 -I 500 -G genome/Saccharomyces.gff -o tophat_yeast15hr genome/Saccharomyces yeast_15hrs_fermentation.fastq
if [ ! -f cufflinks_yeast1hr/genes.fpkm_tracking ]; then
cufflinks -p 4 -o cufflinks_yeast1hr -G genome/Saccharomyces.gff tophat_yeast1hr/accepted_hits.bam
if [ ! -f cufflinks_yeast15hr/genes.fpkm_tracking ]; then
cufflinks -p 4 -o cufflinks_yeast15hr -G genome/Saccharomyces.gff tophat_yeast15hr/accepted_hits.bam
if [ ! -f cuffdiff/genes_expr.diff ]; then
cuffdiff -p 4 -o cuffdiff genome/Saccharomyces.gff tophat_yeast1hr/accepted_hits.bam tophat_yeast15hr/accepted_hits.bam -L Yeast_1hr,Yeast_15hr