Question: basic question cuffdiff
gravatar for vm.higareda
23 months ago by
vm.higareda20 wrote:


I am running cuffdiff but I have a doubt with the -b option

-b/–frag-bias-correct <genome.fa>

According to the manual

-b "Providing Cufflinks with the multifasta file your reads were mapped to via this option instructs it to run our bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates"

I mapped my reads ( illumina-single end) with hisat2 to one index from the genome.fa (the whole genome), not from an index of a multi fasta genome.

So in -b option my input is the genome.fa (whole genome) or I have to do a multi fasta from my genome.fa

Thank you..

ADD COMMENTlink written 23 months ago by vm.higareda20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1390 users visited in the last hour