SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Typical TopHat/Cufflinks pipeline? Aurelien Mazurie Bioinformatics 5 08-02-2012 12:23 AM
Bowtie2 in the Tophat/Cufflinks pipeline? jdanderson Bioinformatics 1 12-30-2011 06:10 AM
Cufflinks pipeline for splicing differences between animal samples seqhorn Bioinformatics 0 07-08-2011 01:23 AM
issues found in using cufflinks/cuffcompare/cuffdiff sterding Bioinformatics 5 06-01-2011 08:04 PM
gsMapper issues mjleaks 454 Pyrosequencing 1 05-12-2009 06:13 AM

Reply
 
Thread Tools
Old 04-09-2012, 04:54 PM   #1
gcoppola
Junior Member
 
Location: New Haven, CT (USA)

Join Date: Nov 2011
Posts: 2
Cool cufflinks/gencode pipeline issues

Hi everyone,

I am trying to use Gencode (ver 7) to do my RNA-seq analysis, but I am having various issues.

1) if I use Gencode as downloaded from the Project website, cufflinks runs for ever. As a comparison, if I use the Ensambl release (using the latest version linked from cufflinks website), the run time is at least 20 times shorter.
Why is there such a huge difference ? just a matter of annotation size ??

2) The original fastq files were mapped (by someone else) with Tophat and using a filtered version of Gencode (it is much smalle than the original).
Is there a problem if I now run cufflinks on the full version of Gencode ?
Intuitively I may expect some loss of accuracy in whatever was filtered out of the full Gencode (given that Tophat ran on a filtered version)

3) Gencode has various duplicated entries. While Tophat and cufflinks do not seem to mind, cuffmerge and cuffcompare exit with an error.
How to solve this issue ?
I guess one can filter the duplicated entries with gffread from either the annotation itself or the transcript.gtf files ???

4) I also ran cufflinks with Ensambl (linked from the cuflinks website), but the resulting transcript.gtf, genes.fpkm_tracking, and isoforms.fpkm_tracking do not have any gene (or transcript) symbol, rather all have the prefix CUFF. What is the problem ? How do I get back the gene symbols ?? could I use cuffmerge ?

Thanks
Gianfilippo
gcoppola is offline   Reply With Quote
Reply

Tags
cufflinks, ensambl, gencode, tophat

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 06:12 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO