Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
htseq-count output for DESeq frymor Bioinformatics 1 10-12-2013 02:41 AM
Output of HTseq-count? kasutubh Bioinformatics 8 08-21-2012 11:39 PM
htseq-count error sissi Bioinformatics 0 03-21-2012 12:40 AM
htseq-count output Palgrave Bioinformatics 7 03-05-2012 08:04 AM
htseq count missing last mapped fragment mapardo RNA Sequencing 2 11-08-2011 06:27 AM

Thread Tools
Old 11-27-2013, 10:09 AM   #1
Location: Philadelphia, PA

Join Date: Aug 2013
Posts: 14
Default Cuffmerge output with missing strand information, htseq-count error

Hi everyone,

I used cuffmerge to obtain a merged.gtf file but there are 3700 entries in my merged.gtf file that contain '.' in the strand field instead of '+' or '-'. I checked the entries that do not have a strand information and each of these have a class-code "u" which stands for unknown.
I want to use this merged.gtf file in my htseq-count command to get the counts (I eventually plan to do a differential gene expression analysis). When I use htseq-count using merged.gtf I get the following error:

Error occured when processing GFF file (line 360833 of file ./merged_asm/merged.gtf):
Feature XLOC_003190 at chr1:[1285003,1285358)/. does not have strand information but you are running htseq-count in stranded mode. Use '--stranded=no'.
[Exception type: SystemExit, raised in]
I know the error is due to missing strand information. I have two options here:

1) Use --stranded=no
2) Remove all the entries corresponding to missing strand information

What do you guys suggest I do? Do you think removing entries with missing information is better than using --stranded=no? I am worried that using --stranded=no will affect the resulting counts, right? Are there any other suggestions?

FYI, I have posted this question on Biostars too:
Komal Rathi
Bioinformatics Application Developer
University of Pennsylvania

Last edited by komalsrathi; 11-27-2013 at 12:21 PM.
komalsrathi is offline   Reply With Quote
Old 11-27-2013, 02:00 PM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Were the libraries directional to begin with and did you tell cufflinks that?
dpryan is offline   Reply With Quote

cuffmerge, htseq-count

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 07:31 PM.

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