Start tophat-cufflinks by submitting to lonestar
0. Make sure all the required modules are loaded.
module load bowtie module load tophat module load cufflinks/2.0.2
1. Copy over the directory $BI/ngs_course/tophat_cufflinks_enrichment to $SCRATCH and cd into that directory.
2. Create a file called tophat.commands with tophat commands. You can use your favorite editor (like nano or emacs) to open and edit a file.
tophat -p 8 -G reference/genes.gtf -o C1_R1_thout reference/genome data/GSM794483_C1_R1_1.fq data/GSM794483_C1_R1_2.fq tophat -p 8 -G reference/genes.gtf -o C1_R2_thout reference/genome data/GSM794484_C1_R2_1.fq data/GSM794484_C1_R2_2.fq tophat -p 8 -G reference/genes.gtf -o C1_R3_thout reference/genome data/GSM794485_C1_R3_1.fq data/GSM794485_C1_R3_2.fq tophat -p 8 -G reference/genes.gtf -o C2_R1_thout reference/genome data/GSM794486_C2_R1_1.fq data/GSM794486_C2_R1_2.fq tophat -p 8 -G reference/genes.gtf -o C2_R2_thout reference/genome data/GSM794487_C2_R2_1.fq data/GSM794487_C2_R2_2.fq tophat -p 8 -G reference/genes.gtf -o C2_R3_thout reference/genome data/GSM794488_C2_R3_1.fq data/GSM794488_C2_R3_2.fq
3. Create a file called cufflinks.commands with cufflinks commands. You can use your favorite editor (like nano or emacs) to open and edit a file.
cufflinks -p 8 -o C1_R1_clout C1_R1_thout/accepted_hits.bam cufflinks -p 8 -o C1_R2_clout C1_R2_thout/accepted_hits.bam cufflinks -p 8 -o C1_R3_clout C1_R3_thout/accepted_hits.bam cufflinks -p 8 -o C2_R1_clout C2_R1_thout/accepted_hits.bam cufflinks -p 8 -o C2_R2_clout C2_R2_thout/accepted_hits.bam cufflinks -p 8 -o C2_R3_clout C2_R3_thout/accepted_hits.bam
4. Alternatively, lets put tophat and cufflinks in one command file and make sure they run sequentially. Lets call this file tc.commands
tophat -p 8 -G reference/genes.gtf -o C1_R1_thout reference/genome data/GSM794483_C1_R1_1.fq data/GSM794483_C1_R1_2.fq && cufflinks -p 8 -o C1_R1_clout C1_R1_thout/accepted_hits.bam tophat -p 8 -G reference/genes.gtf -o C1_R2_thout reference/genome data/GSM794484_C1_R2_1.fq data/GSM794484_C1_R2_2.fq && cufflinks -p 8 -o C1_R2_clout C1_R2_thout/accepted_hits.bam tophat -p 8 -G reference/genes.gtf -o C1_R3_thout reference/genome data/GSM794485_C1_R3_1.fq data/GSM794485_C1_R3_2.fq && cufflinks -p 8 -o C1_R3_clout C1_R3_thout/accepted_hits.bam tophat -p 8 -G reference/genes.gtf -o C2_R1_thout reference/genome data/GSM794486_C2_R1_1.fq data/GSM794486_C2_R1_2.fq && cufflinks -p 8 -o C2_R1_clout C2_R1_thout/accepted_hits.bam tophat -p 8 -G reference/genes.gtf -o C2_R2_thout reference/genome data/GSM794487_C2_R2_1.fq data/GSM794487_C2_R2_2.fq && cufflinks -p 8 -o C2_R2_clout C2_R2_thout/accepted_hits.bam tophat -p 8 -G reference/genes.gtf -o C2_R3_thout reference/genome data/GSM794488_C2_R3_1.fq data/GSM794488_C2_R3_2.fq && cufflinks -p 8 -o C2_R3_clout C2_R3_thout/accepted_hits.bam
5. We have a commands file. We need a launcher file to submit this to the lonestar queue. Use launcher_creator.py to create a launcher file.
6. Submit this job to the queue.
7. Create a file called cuffmerge.commands to run cuffmerge on results from step 6.
nano cuffmerge.commands cuffmerge -g reference/genes.gtf -s reference/genome.fa -p 8 assembly_list.txt
8. Use launcher_creator to create a launcher for this cuffmerge job and submit it to the queue such that it runs after the previous job completes.
launcher_creator.py -n cuffmerge -q normal -t 6:00:00 -j cuffmerge.commands -l cuffmerge_launcher.sge qstat qsub -hold_jid <jobid> cuffmerge_launcher.sge
9. Create a file called cuffdiff.commands to run cuffdiff on results from step 7.
nano cuffdiff.commands cuffdiff -o diff_out -b reference/genome.fa -p 8 -L C1,C2 -u merged_asm/merged.gtf C1_R1_thout/accepted_hits.bam,C1_R2_thout/accepted_hits.bam,C1_R3_thout/accepted_hits.bam C2_R1_thout/accepted_hits.bam,C2_R2_thout/accepted_hits.bam,C2_R3_thout/accepted_hits.bam
10. Use launcher_creator to create a launcher for this cuffdiff job and submit it to the queue such that it runs after the previous job completes.
launcher_creator.py -n cuffdiff -q normal -t 6:00:00 -j cuffdiff.commands -l cuffdiff_launcher.sge qsub -hold_jid <jobid> cuffdiff_launcher.sge
