Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Tablet not showing pileup indels

    Hi,

    I have a pileup file with the following line:
    Code:
    chr4	103518793	*	*/+TA	20	20	33	6	*	+TA	5	1	0	0	0
    I understand this implies that there is an indel at position 103518793 on chr4. However, upon opening the bam file in tablet and checking said location, I see 6 reads, none of which support an indel.

    Does anyone know what might cause this?

    Thanks.

  • #2
    Tablet does not display insertions by putting a gap in the reference sequence, but by putting an annotation in a feature track running alongside the alignment. This is the "CIGAR-I" track (if you don't have it by default you should be able to add it in "Select Tracks" in the "Features" tab) - an insertion is marked by a big "I" in this track, hoover the "I" and it shows you what read(s) have the insertion.

    It works but it's a bit awkward in my opinion. Having an option for displaying gaps in the reference sequence (like in e.g. samtools tview) would be pretty neat.

    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
    12 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    10 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
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X