Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • TopHat: output is not recognized by UCSC

    Hi, we ran TopHat without a GFF3 file and the output does not appear to be recognizable wiggle and bed formats. Here is what we got (first lines) of the wiggle file:
    track type=bedGraph name="TopHat - read coverage"
    gi|149258597|ref|NT_039457.7|Mm8_39497_37 0 46627 0
    gi|149258597|ref|NT_039457.7|Mm8_39497_37 46627 46667 1
    gi|149258597|ref|NT_039457.7|Mm8_39497_37 46667 48587 0
    gi|149258597|ref|NT_039457.7|Mm8_39497_37 48587 48627 1

    And here is what we got from the bed file:
    track name=junctions description="TopHat junctions"
    gi|149258597|ref|NT_039457.7|Mm8_39497_37 1132498 1133665 JUNC00000001
    13 + 1132498 1133665 255,0,0 2 31,21 0,1146
    gi|149258597|ref|NT_039457.7|Mm8_39497_37 1264693 1270688 JUNC00000002
    39 + 1264693 1270688 255,0,0 2 32,32 0,5963

    The program ran without errors. We think that there is a step missing that would associate the gi/NTs to chromosome coordinates. We are thus wondering what will be the way to work through this.. Is it because of the missing GFF3 file? (we could not find one for mouse, and if this is a problem, we would appreciate some pointers on how to make one) Any other suggestions?

    Thanks very much in advance!
    Last edited by geriatrics1200; 06-03-2009, 08:43 AM.

  • #2
    I had the same problem before. What you need to do is to make your own bowtie index file using 'bowtie-build' command on fa files you downloaded from UCSC site.

    Hope it helps,
    Statsteam

    Comment


    • #3
      Yep, the same I heard from author

      UCSC recognizes nothing but chr#, so have to you build your own indexes on chromosome sequences, which can downloaded from UCSC.

      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