SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Zero fpkm estimation using cuffquant/cuffnorm (Cufflinks 2.2.1) Rainbird Bioinformatics 2 02-17-2015 05:46 PM
Cufflinks skips transcript models in regions with abundant reads mcbiodude Bioinformatics 1 08-12-2013 10:44 AM
CuffDiff: genes with highly abundant reads have FPKM 0. uniportdb Bioinformatics 3 02-16-2013 10:09 PM

Reply
 
Thread Tools
Old 02-06-2019, 04:19 PM   #1
capricy
Senior Member
 
Location: 63130

Join Date: Apr 2012
Posts: 124
Default cuffnorm (from cufflinks package) masks highly abundant genes???

I compared the cuffnorm FPKM outputs with cuffdiff FPKM outputs for the same sets of samples, and found that some highly abundant genes identified by cuffdiff were actually shown to be 0 in cuffnorm outputs.

Has anyone had the similar issue?

Thanks.

C.
capricy is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:08 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO