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RNA-Seq workflow

November 12, 2012 in Problem Sets

I have posted RNA-Seq pipeline script you can use to run the RNA-Seq analysis with TopHat and Cufflinks on the yeast 1hr and 15hr fermentation time points.

https://github.com/hyphaltip/htbda_perl_class/blob/master/examples/NGS/all_commands_RNASeq.sh

Try and figure out how many genes are differentially expressed between these two time points – look in the cuffdiff folder that will be produced.

Remember to run this as a qsub job by doing

qsub -d `pwd` all_commands_RNASeq.sh

you don’t have to run it in the same directory as the checked out script but you can if you like. This will create a folder of about 3Gb in total so make sure you have enough space when you are running this.

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