Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
gff3,gtf to gff parulvk Bioinformatics 2 11-15-2011 11:48 AM
Cufflinks' computation of FPKM for --GTF and --GTF-guide estimation burt Bioinformatics 0 08-23-2011 11:59 PM
Ensembl gtf to gff3 for tophat genec Bioinformatics 16 05-29-2011 09:15 PM
Looking process to convert gff3 format into ace format or sam format andylai Bioinformatics 1 05-17-2011 02:09 AM
cufflinks -G gff/gtf format guangxiwu Bioinformatics 0 04-22-2011 09:43 AM

Thread Tools
Old 07-28-2011, 06:40 AM   #1
Location: Virginia

Join Date: Oct 2010
Posts: 12
Default GTF/GFF3 format and new Cufflinks

Hi all,

I have sucessfully completed an RNAseq pipeline with the old version of Cufflinks and I'm now trying to run the same data through the new versions of Tophat and Cufflinks. Namely, I'm hoping to add on all the bells and whistles of the new Cufflinks (bias correction, multi-read correct, and RABT).

My problem seems to be in implementing the RABT portion of Cufflinks. I suspect it might be a problem with the format of my GFF3 annotation. Could anyone who has successfully run the new version of Cufflinks please post a few lines of their annotation file?

Also, for researchers working on "more" complete genomes, how did you handle the completed-ness of the genome annotation vs. the increase in false-positives as was mentioned in the Roberts et al paper describing RABT?

Any help would be GREATLY appreciated!!!
ega2d is offline   Reply With Quote
Old 07-28-2011, 10:44 AM   #2
Senior Member
Location: East Coast, US

Join Date: Jun 2010
Posts: 177


Check this link ( if you have not. The tool gffread can help you verify if your GFF3 annotation is in the right format.

Hope this helps.

DZhang is offline   Reply With Quote
Old 08-02-2011, 01:40 PM   #3
Senior Member
Location: Boston

Join Date: Nov 2009
Posts: 224

Illumina is now hosting index and annotation files suitable for Tophat/Cufflinks for several genomes. You can get them here:
pbluescript is offline   Reply With Quote
Old 06-30-2013, 06:54 PM   #4
Junior Member
Location: china

Join Date: Jun 2013
Posts: 1

hi,newcomers ....eager to learn from you
windowon is offline   Reply With Quote

cufflinks, gff3, rabt

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 06:27 AM.

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