Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • JIGSAW gene prediction combiner - use for prokaryotes?!

    Hi, I have a recently assembled bacterial genome. It consists of a a couple dozens scaffolds, and I have put them through three gene prediction methods: Prodigal, Glimmer, and GeneMark.

    Now that I have three different gtf files describing putative genes, I want to somehow combine these results into a consensus list. I have been looking into such a combiner called JIGSAW and was wondering if anyone has experience using this software with bacteria (I think it was made with eukarylotes in mind).

    I am running with the following command:

    jigsaw -l -f "myGenome.fasta" -m "jigsaw.output" -e "myEvidenceFile"

    And my evidence file looks like this:

    scaffolds_GeneMark.gff gff geneprediction coding 1.0
    scaffolds_Prodigal.gff gff geneprediction coding 1.0
    scaffolds_Glimmer.gff gff geneprediction coding 1.0

    Typically, JIGSAW wants the user to provide the type of exon that was annotated (start, internal, end, etc), but since this is a prokaryote, I thought maybe it was best just to use the "coding" identifier.

    The problem is, for a particular contig that has an average of 10 genes predicted from each individual method (7 of which overlap perfectly between all three methods), JIGSAW is only predicting 2 genes!

    Any comments or suggestions and much appreciated

  • #2
    I did the same. I predicted ORFs in a complete bacteria genome by glimmer, genemark and prodigal. However, how I can integrate all this information and decide which ORFs are the most probables ones and which ones are not?

    Comment


    • #3
      Look on Pubmed for "Reganor", I remember this software does exactly this combination of different gene prediction tools.

      Best,
      Loddi

      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
      49 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