Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • ^@ in .combined.gtf from cuffcompare v0.8.4

    Hi,

    after cufflinks generates tnp1/transcripts.gtf tmp2/transcripts.gtf (attached: tmp_gtf.zip)

    I run cuffcompare (attachted: combined_gtf.zip) to generate a .combined.gtf from both of these .gtf files by

    > cuffcompare -p 5 tmp1/transcripts.gtf tmp2/trascripts.gtf

    > less stdout.combined.gtf
    "stdout.combined.gtf" may be a binary file. See it anyway?

    column 7, which should be "strand" from GTF, is presented by a weired "^@" character.

    Currently, I replace this column by "." .

    I am wondering if anybody met the same problem before. Maybe Cole can help to explain?!

    tmp_gtf.zip

    combined_gtf.zip

  • #2
    Originally posted by glacierbird View Post
    Hi,

    after cufflinks generates tnp1/transcripts.gtf tmp2/transcripts.gtf (attached: tmp_gtf.zip)

    I run cuffcompare (attachted: combined_gtf.zip) to generate a .combined.gtf from both of these .gtf files by

    > cuffcompare -p 5 tmp1/transcripts.gtf tmp2/trascripts.gtf

    > less stdout.combined.gtf
    "stdout.combined.gtf" may be a binary file. See it anyway?

    column 7, which should be "strand" from GTF, is presented by a weired "^@" character.

    Currently, I replace this column by "." .

    I am wondering if anybody met the same problem before. Maybe Cole can help to explain?!

    [ATTACH]459[/ATTACH]

    [ATTACH]460[/ATTACH]
    This is most likely due to the status of the v0.8.4 (svn r1370, 16-Jul-2010). Cole has provided this snapshot prerelease to overcome the "duplicate gff id" errors introduced in v0.8.3 (discussed in http://seqanswers.com/forums/showpos...90&postcount=7).

    Best,
    Uwe

    Comment


    • #3
      I went back and forth about rehashing an old thread or starting a new one, so my apologies if this is against board etiquette.

      I have been getting a similar error with Bowtie 0.12.7, TopHat 1.1.4, and Cufflinks 0.9.3. The strand column in the *combined.gtf file created by cuffcompare occasionally has a ^@ instead of a + or -. The most frustrating thing about it is that I'm unable to upload it to the UCSC browser.

      glacierbird, if you're still listening, would you be able to tell me how you replaced all these characters? I've tried using sed, grep, regex in perl, vi, emacs, gedit, and a few OpenOffice programs.

      Uwe, do you know if this problem was the result of this duplicate gff error and if it was supposed to be corrected in the latest versions?

      Many thanks.

      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, 03-27-2024, 06:37 PM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-27-2024, 06:07 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      53 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X