Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Training Augustus with tophat

    I've got two lanes of Illumina 120x120 cDNAs and a ~70Mb denovo assembled genome. I'd like to train augustus using the .bam alignments of said transcripts to said genome. The webpage reads thusly:

    In lack of a better program, we chose to use the program BLAT, which is not customized for NGS reads (Next Generation Sequencing), but found more introns than Tophat 1.0.11. However, it is straightforward to adjust this pipeline to Bowtie/Tophat input, because Tophat produces results in the same or similar format (wig file and intron list including multiplicities).

    I'm a bit confused regarding this as I don't believe either .wig files or intron lists are part of the tophat output. Has anyone done this?

    I have no problem using BLAT as well, however I've already spent 3 days of cluster horsepower on tophat.

    Thanks!

  • #2
    k-gun12, the information you are looking for is on accepted_hits.sam and junctions.bed (fort the intron positions)

    Youl could go from sam to wig using a sam2wig script you can find on the web (I have downloaded this before, but could not remember where). The information you need to find the intron positions is in junctions.bed, but I don't know any script for conversion, in this case. However, it is not difficult to write a script to accomplish this conversion.

    I would suggest to filter out junctions supported by only 1 read, as many of them are false positive.

    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