Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • behaviour of bwa mapping for homologous regions.

    Hi
    I am using bwa on paired end illumina reads for identifying inter chromosomal translocation.
    I have used breakdancer on the data but non of the proposed inter chromosomal translocations match what I have on my list of suspects (garnered from FISH)

    I am looking at the alignment of the regions now manually and I find that there is low coverage in this region.

    I am suspecting that the translocation are taking place in homologous regions within the genome.
    Would this cause reads to be 'dropped out' from the final bam file if bwa finds equally plausible regions which the read might map?

    How should I hunt for evidence for the translocation?
    http://kevin-gattaca.blogspot.com/

  • #2
    BWA just chooses a random best alignment if there are several equally scoring best alignments. Hence I think your suspicion is the most probable explanation for not finding the translocation with NGS data that you've seen with FISH. A colleague had a similar problem with a paralogous gene.

    BFAST has an option to keep all possible alignments for a read, I think that also works with paired end data. (I'm sure Nils will be helpful in this aspect.) Then the same read ID will appear multiple times in the SAM file and you have to think of a way for filtering with your own criteria.

    Barbara

    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
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    8 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
    66 views
    0 likes
    Last Post seqadmin  
    Working...
    X