Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bismark paired-end positions

    Hello,

    I noticed that Bismark paired-end runs give you an output with start/stop genomic positions only for the first read, but not for its mate.

    As the two mates overlap but do not have identical start/stop positions, is there a recommended way to discern the start/stop position of the second read, without having to re-align it to the genome or to its mate?

    I'm aware that methylation_extractor takes care of this, but I'd be interested in the full sequence of paired-end runs in addition to the methylation call.

    Any suggestions would be greatly appreciated!

  • #2
    Originally posted by mixter View Post
    Hello,

    I noticed that Bismark paired-end runs give you an output with start/stop genomic positions only for the first read, but not for its mate.

    As the two mates overlap but do not have identical start/stop positions, is there a recommended way to discern the start/stop position of the second read, without having to re-align it to the genome or to its mate?

    I'm aware that methylation_extractor takes care of this, but I'd be interested in the full sequence of paired-end runs in addition to the methylation call.

    Any suggestions would be greatly appreciated!
    Hi Mixter,

    the older output format (now called vanilla) does not report the start and end positions of the first read but of the the read pair as a whole. If you want to get the individual start end positions of each read it would be start + length (read1) or end - length(read2)+1.

    The latest versions of Bismark (0.6.x) can also output SAM format, in which every read is reported on a separate line, so it is quicker to see where each of the reads was aligned. And just for the record, reads that overlap perfectly are not considered a valid alignment by Bowtie (this is intentional) and are thus not reported at all.

    Hope this helps,
    Felix

    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
    50 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