SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Q values in cuffdiff with 2 biological replicates nr23 Bioinformatics 1 02-20-2014 06:47 PM
cuffdiff (v 2.1.1) p-values nsl Bioinformatics 4 06-03-2013 09:25 PM
cuffdiff q values jk1124 RNA Sequencing 4 01-04-2013 08:38 AM
Galaxy Cuffdiff Values ccard28 Bioinformatics 1 09-05-2012 06:52 AM
Cuffdiff producing q-values > 1 ocs Bioinformatics 7 08-15-2012 10:26 AM

Reply
 
Thread Tools
Old 01-19-2014, 01:59 PM   #1
jake13
Member
 
Location: San Francisco

Join Date: Aug 2013
Posts: 23
Default cuffdiff dispersion cutting off low values

I've been running cuffdiff on some paired end rna seq samples with biological replicates. Before I started analyzing them I checked the dispersion plots using cummeRbund. For some reason it is forming a sharp cutoff which looks different from the examples on the websites. I have tried mapping both with tophat2.0.9 and STAR aligner and got identical results.

I have been using cuffdiff with the default options except for -b and using the genes.gtf file provided by the Illumina iGenomes download. Does anyone have ideas on what might be going wrong?
Thanks
Attached Images
File Type: gif cuffdiff_problem.gif (33.7 KB, 10 views)
jake13 is offline   Reply With Quote
Old 01-23-2014, 08:07 PM   #2
jake13
Member
 
Location: San Francisco

Join Date: Aug 2013
Posts: 23
Default

An update for anyone else running into this problem. It seems to be caused by the gtf file that I was using. I tried grabbing the refseq gtf file from the UCSC table browser as well as the genes.gtf fill that's included in the Illumina iGenomes package. I ran identical reads with identical settings through tophat/cuffdiff except for using these two different gtf files. The UCSC one is on the left and looks correct, the iGenomes one is on the right and has the weird cutoff. I have no idea why this is occurring. Does anyone have any thoughts?
Attached Images
File Type: png cuffdiff_gtf_comparison.png (88.9 KB, 9 views)
jake13 is offline   Reply With Quote
Old 08-05-2016, 05:01 AM   #3
blouro
Junior Member
 
Location: edinburgh

Join Date: Sep 2008
Posts: 4
Default

Up with this topic, because I'm getting similar problem. Used the Tophat and tuxedo tools pipeline, and now looking at the dispersion plots I'm getting a strange profile in two aspects, the values are way off the expected range, and the dispersion profile seem way zoomed out due to few lower values. Please see attached plot and give me your opinion, it will be much appreciated!

P.s For the cuffdiff analysis I used the merged gtf file created in the cuffmerge step.
Attached Files
File Type: pdf DispPlot_genes.pdf (1.99 MB, 3 views)
blouro 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 02:50 AM.


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