SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
TopHat Issue ashuchawla RNA Sequencing 0 09-10-2013 10:05 AM
tophat with/without annotation,and cufflink with annotation? louis7781x Bioinformatics 19 04-05-2013 07:09 AM
Tophat mapping and Cufflinks issue jimcohen1000 RNA Sequencing 0 01-09-2013 11:28 AM
How to run Tophat with annotation file masylichu Bioinformatics 2 09-06-2011 07:25 PM
TopHat alignment issue telos Bioinformatics 0 03-16-2010 10:39 AM

Reply
 
Thread Tools
Old 09-20-2013, 12:31 AM   #1
rozitaa
Member
 
Location: Sweden

Join Date: Jun 2013
Posts: 51
Exclamation TopHat annotation file issue

Hi,

I am aligning my RNA-seq data by TopHat and I get an error as following:

[2013-09-20 09:30:16] Creating transcriptome data files..
[FAILED]
Error: gtf_to_fasta returned an error.


I have checked the names of gtf and index files are same. Also both files have been downloaded from ensemble (meaning I don't have different format of chromosomes name). When I am using UCSC index and gtf file everything works well. But UCSC doesn't provide genes name but only genes ids. That's why I want to switch to ensembl. I was wondering if you have any idea about this!

Thanks for any help!
rozitaa is offline   Reply With Quote
Old 09-20-2013, 05:25 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

If you look in the run log, you'll see the actual command that's executed. Just try executing that yourself to find out what the real error message is. That'll give you a better idea what went wrong.
dpryan is offline   Reply With Quote
Reply

Tags
annotaion file, 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 11:52 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO