Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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 count.py:59]
    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:http://www.biostars.org/p/87578/
    Last edited by komalsrathi; 11-27-2013, 12:21 PM.
    Komal Rathi
    Bioinformatics Application Developer
    University of Pennsylvania

  • #2
    Were the libraries directional to begin with and did you tell cufflinks that?

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    9 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    51 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X