Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Merge two gff3 files?

    I have two gff3 files, one of primary transcripts and one of alternative transcripts, that need to be merged into one file. Since the files must be interwoven (some gene IDs appear in both), simply concatenating the files won't do.

    Anyone had any experience doing such a thing? I have worked quite a bit with BioPerl but have no experience handling annotations. And feeling lazy this time -- would rather find a tool that already exists than roll my own.

    Thanks much!!
    Bob

  • #2
    Do the annotations really need to be interwoven? I know that it is convention but as far as I know it is not a requirement of the GFF. I think it would only matter if the particular software using the file as input requires it.

    Comment


    • #3
      Not sure what the spec says. I tried to concatenate the two files and use that, but the program I submitted the concatenated file to barfed with the error 'duplicate gene id' (or something like that). So i surmised that it expected to see the gene id defined only once, indicating that the data needs to be interleaved.

      I guess I could try and take a shortcut -- find all those gene ids that are 'duplicates', remove those 'gene' lines from the 2nd file, and concatenate. Probably about 10 minutes of work...

      -Bob

      Comment


      • #4
        How about BEDtools 'intersectbed'. It works with gff.

        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
        69 views
        0 likes
        Last Post seqadmin  
        Working...
        X