SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
cuffdiff: use merged.gtf from cuffmerge or combined.gtf from cuffcompare? turnersd Bioinformatics 21 10-02-2014 03:41 AM
Does the transcripts.gtf in cuffdiff is the output of cufflinks? camelbbs Bioinformatics 0 10-22-2011 06:09 PM
Cufflinks' computation of FPKM for --GTF and --GTF-guide estimation burt Bioinformatics 0 08-23-2011 11:59 PM
cuffdiff gtf input from cufflinks? PFS Bioinformatics 1 03-24-2011 12:46 PM
GTF file for cuffdiff 0.9.1 kalidaemon Bioinformatics 7 11-15-2010 09:26 AM

Reply
 
Thread Tools
Old 06-07-2010, 11:24 AM   #1
Bio.X2Y
Member
 
Location: Europe

Join Date: Apr 2010
Posts: 46
Default CuffLinks / CuffDiff GTF Compatibility

Hi,

I want to use CuffDiff to call DE between two samples that I've aligned with TopHat.

Rather than creating a GTF via CuffLinks, I used one from UCSC (RefSeq). Since the manual suggests the GTF can be from sources other than CuffLinks, I assume this isn't a problem?

One thing that confuses me, however, is that CuffLinks seems to creating 0-based coordinates in its GTF (as per manual), while the GTF 2.2 standard calls for 1-based coordinates.

Since the UCSC GTF uses 1-based, does that mean UCSC GTF files are incompatible with CuffDiff?

Thanks,
Bio

Last edited by Bio.X2Y; 06-07-2010 at 11:26 AM. Reason: Got my 0s and 1s mixed up...
Bio.X2Y is offline   Reply With Quote
Old 06-16-2010, 07:24 AM   #2
Bio.X2Y
Member
 
Location: Europe

Join Date: Apr 2010
Posts: 46
Default

I've raised this question on the Bowtie sourceforge (I can't find a place to raise CuffLinks specific questions/bugs):
https://sourceforge.net/tracker/?fun...7&atid=1101606

Text:
Am I correct in thinking that the CuffLinks GTF files are non-standard? They use 0-based coordinates as per the manual, while GTF2.2 requires 1-based. Does this mean that CuffDiff is not compatible with UCSC or Ensembl GTFs?
Bio.X2Y is offline   Reply With Quote
Old 08-17-2011, 08:04 AM   #3
Marcelo_Alejandro
Junior Member
 
Location: United States

Join Date: May 2011
Posts: 1
Default

While describing the start column of the transcripts.gtf file, cufflinks manual (http://cufflinks.cbcb.umd.edu/manual...fflinks_output) states:

Quote:
The leftmost coordinate of this record (where 1 is the leftmost possible coordinate)
Therefore, it should be 1-based.

Last edited by Marcelo_Alejandro; 08-17-2011 at 11:55 AM.
Marcelo_Alejandro 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 09:56 AM.


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