SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Inconsistent results of cuffcompare, looking for help weibominingdata Bioinformatics 2 11-09-2011 08:47 PM
cuffcompare only generates .gtf.tmap and .gtf.refmap? julio514 Bioinformatics 4 07-15-2011 04:18 AM
cuffcompare????????? semna Bioinformatics 0 05-15-2011 02:21 AM
refmap empty madsaan Bioinformatics 1 01-25-2011 12:22 PM
To cuffcompare or not to cuffcompare poisson200 Bioinformatics 5 08-08-2010 02:58 AM

Reply
 
Thread Tools
Old 05-28-2012, 03:02 PM   #1
mhadidi2002
Member
 
Location: Germany

Join Date: Jun 2011
Posts: 24
Default Cuffcompare *.refmap results

Hello,

I used cuffcompare to compare a reference GFF file with another cufflinks GFF file. When I looked at the *refmap file, there are 2 possibilities in the third column, = or c. according to the manual, = is fully matched, I supposed that this means that the coordinates are exactely the same; the exact same start and exact same end positions, but unfortunately this wasn't the case.

I would like to know what is the threshold (number of nucleotides) that can be varied between each of the 2 start and 2 end positions of both genes?

Thanks in advance,

Best,
mhadidi2002 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 07:53 AM.


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