SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
CuffDiff output Rachelly Bioinformatics 11 04-17-2012 08:04 PM
Cuffdiff output sheenams RNA Sequencing 0 11-27-2011 03:41 PM
Cuffdiff Output Explanation fongchun Bioinformatics 4 11-08-2011 10:26 AM
cuffdiff output dnusol Bioinformatics 2 02-08-2011 10:31 PM
Cuffdiff output question jdanderson Bioinformatics 1 10-14-2010 08:13 AM

Reply
 
Thread Tools
Old 03-20-2012, 06:57 PM   #1
kasutubh
Member
 
Location: US

Join Date: Mar 2010
Posts: 25
Default cuffdiff output

Hi everyone,

I want to analyze data using cummeRbund but I'm having problem with cuffdiff output. I don't get any entries in the gene_id and gene columns in the output files of cuffdiff. Also all the other files except isoform_exp.diff, isoform.FPKM_tracking are blank. When I specify file into the cummeRbund, I get following output,
CuffSet instance with:
2 samples
0 genes
0 isoforms
0 TSS
0 CDS
0 promoters
0 splicing
0 relCDS
What might be the problem here? I would really appreciate any help in this regard.
Thanks in advance!
kasutubh is offline   Reply With Quote
Old 07-30-2013, 06:46 PM   #2
jp.
Senior Member
 
Location: NikoNarita.jp

Join Date: Jul 2013
Posts: 142
Question

did you get solution? I got same and psoted here :
http://seqanswers.com/forums/showthr...110#post112110

may expect your view ?
Thank you


Quote:
Originally Posted by kasutubh View Post
Hi everyone,

I want to analyze data using cummeRbund but I'm having problem with cuffdiff output. I don't get any entries in the gene_id and gene columns in the output files of cuffdiff. Also all the other files except isoform_exp.diff, isoform.FPKM_tracking are blank. When I specify file into the cummeRbund, I get following output,
CuffSet instance with:
2 samples
0 genes
0 isoforms
0 TSS
0 CDS
0 promoters
0 splicing
0 relCDS
What might be the problem here? I would really appreciate any help in this regard.
Thanks in advance!
jp. is offline   Reply With Quote
Reply

Tags
cuffdiff, cummerbund

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 03:29 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO