How to calculate all transcripts from cufflinks

Question

[Paul]

Dear all,

I have two mouses paired-end sequenced. I mapped with Tophat2 - make Cufflinks - and Cufdiff (one replicates - two conditions) - and CummeRbund. It is very nice graphs and outputs, but I would like to get just one number, which describe me total transcript expression for mouse1 and for mouse2 and compare it.

It is possible to take output form Cufflinks - transcripts.gtf and extract FPKM value for all genes and do sum of all FPKM's? Something like - awk 'OFS="\t"{sum+=$16}END {print sum}' transcripts.gtf.

Thank you so much for explanation and help,

Paul.

Answer 1

[Paul]

Answer is pretty easy - just print the FPKM > 0 from isoforms.fpkm_tracking file.

So it could be:

awk '{if ($10>0) print $0}' isoforms.fpkm_tracking | awk 'OFS="\t" {print $1,$4,$6,$7,$8}' | awk 'END{print NR}'

This tell us how many isoforms we have.