Question: How to calculate all transcripts from cufflinks
gravatar for Paul
6.6 years ago by
European Union
Paul1.4k wrote:

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,



rna-seq cufflinks fpkm • 2.1k views
ADD COMMENTlink modified 6.4 years ago • written 6.6 years ago by Paul1.4k
gravatar for Paul
6.4 years ago by
European Union
Paul1.4k wrote:

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.

ADD COMMENTlink written 6.4 years ago by Paul1.4k
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