SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
cufflinks FPKM >>> Cuffdiff FPKM peromhc Bioinformatics 6 10-17-2012 02:07 PM
Zero FPKM at some Cufflinks output file fuad193 Bioinformatics 1 06-07-2012 12:16 AM
Question to combine Bowtie output with Tophat's -- impact on Cufflinks FPKM values berath Bioinformatics 0 04-21-2011 09:38 AM
instructing cufflinks to use more than one thread MatthewVC Bioinformatics 3 06-24-2010 05:19 PM
help on Cufflinks output: individual exon have same FPKM clariet Bioinformatics 2 05-03-2010 10:38 AM

Reply
 
Thread Tools
Old 07-20-2012, 11:35 AM   #1
Rachel Hillmer
Junior Member
 
Location: Minneapolis, MN

Join Date: Jun 2012
Posts: 8
Default Cufflinks FPKM output not consistent with different thread numbers

Hi,

I find that the FPKM values cufflinks prints out when I run it with multiple threads (p -5) are about 4 orders of magnitude higher than when I run cufflinks in a single-processor mode (p -1, or unspecified since 1 is the default).

Is anyone else having this problem?

This happens regardless of which cufflinks version I'm using (1.3.0 or 2.0.2).

Cheers,
~Rachel
Rachel Hillmer is offline   Reply With Quote
Old 07-23-2012, 04:27 PM   #2
Rachel Hillmer
Junior Member
 
Location: Minneapolis, MN

Join Date: Jun 2012
Posts: 8
Default

The above is an incorrect report. I happened to also be changing whether or not quartile normalization was being used concurrently with additional threads. Further investigation reveals that this huge change in FPKMs (~4 orders of magnitude) is directly linked to quartile normalization. That's still confusing, but I'm starting a new thread for that, with a more appropriate title.
Rachel Hillmer 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 07:19 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO