Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Tophat mapping Results

    Hi All

    I used tophat to map my 100 million base paired illumina reads after trimming with average length of 86 bp. In the bam output file generated by tophat I only find around 55 million read mapped and around 42 million reads unmapped. Can any one tell me that is it a feasible number in case of mammals.
    Also what can be the reason on so much of unmapped reads since I have already cleaned the data with q value 30 and removed the adapters and primers.
    In this paper http://www.plosone.org/article/info%...l.pone.0046415 I see that the comparison of topaht with GSNAP where tophat has very low mapping reads

    Regards

  • #2
    1) What are the commands you ran Tophat with?
    2) What is your reference? I don't think one can generalize about mammals or plants or anything like that.
    3) What I always like to do when I have a lot of unmmapped reads is take a random selection of those reads and just Blast them and see what pops up. For example, I once had some reads with a lot of adapter sequence in the 3' end. I found that out when my Blast results showed that only part of the read matched my reference. I have also worked with libraries with a lot of reads from the mitochondria, for which I did not have a completed genome for. I know this only because I blasted those reads to see what they might be.

    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