Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • shurjo
    Senior Member
    • Jan 2009
    • 132
    #1

    GFF3 file format for TopHat

    Hello everyone,

    I just used gtf2gff3 to convert the UCSC knownGenes GTF file to GFF3 format and would like to use this as the supplied annotation for a TopHat run. Now, according to the TopHat manual, "Transcript records are called "mRNA", not "transcript"." However, in the GFF3 file I just created, both the "mRNA" and "transcript" SOFA terms are present. Specifically, here are the counts:

    488996 CDS
    612391 exon
    93721 five_prime_utr
    66803 gene
    53036 mRNA
    53036 start_codon
    13767 transcript

    Does anyone have experience with this situation and can tell me if TopHat will work with this file?

    Thanks,

    Shurjo
    Tags: None
    Previous template Next

    Latest Articles

    Collapse
    • SEQadmin2
      Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
      by SEQadmin2



      Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

      Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating      ...
      10-14-2026, 09:55 AM
    • SEQadmin2
      New Genomics Technologies Take Aim at Long-Standing Limits
      by SEQadmin2


      Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

      We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing      ...
      09-28-2026, 10:25 AM
    View All

    ad_right_rmr

    Collapse

    News

    Collapse
    Topics Statistics Last Post
    Exeter-Led Study Maps What an Average Human Genome Looks Like by SEQadmin2
    Started by SEQadmin2, Yesterday, 11:13 AM
    0 responses
    16 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    Yesterday, 11:13 AM  
    Long-Read Sequencing Uncovers Cancer Mutations Conventional Testing Missed by SEQadmin2
    Started by SEQadmin2, Yesterday, 10:48 AM
    0 responses
    18 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    Yesterday, 10:48 AM  
    Mayo Clinic-Led Study Detects DNA Mutations Across Noncancerous Tissues by SEQadmin2
    Started by SEQadmin2, 10-15-2026, 10:52 AM
    0 responses
    35 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    10-15-2026, 10:52 AM  
    Study Finds Chromatin Motion Holds Steady Until Cells Face Stress by SEQadmin2
    Started by SEQadmin2, 10-14-2026, 05:39 AM
    0 responses
    42 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    10-14-2026, 05:39 AM  
    View All
    Working...