I am running an experiment with 4 samples paired-end among 2 conditions (Control vs Mutation) and 2 replicates of each one (C1, C2, MUT1, MUT2).
After mapping with segemehl, I build the transcripts with Cufflinks. So, at the end I have transcripts.gtf, genes.fpkm_tracking and isoforms.fpkm_tracking. Now I have to pick the count (FPKM) of each gene and divide by a certain value corresponding the count of plasmid that was inserted in each sample and then proceed with the pipeline (cuffmerge and cuffdiff).
This values can be found in the table bellow.
But how can I do that? I already tried to edit the output from cufflinks and divide the counts of the 3 files, but when I merge the transcripts, all values disappear. I can't try after runs cuffmerge because the samples are merged and I can't discriminate the samples.
There's a way to do it?