Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • All the CIGAR strings of reads mapped by Bowtie are "I"

    Hi, guys,

    I'm sorry, I make a mistake, there is no problem, but I don't know how to delete the problem.

    -------------------------------------------------------------------------------------------------------

    I faced a problem when mapping again...
    I used Bowtie to align CLIP-seq reads to genome with the parameter "-v 1" which allow the reads have one mismatch. But in the result, Bowtie treat all the nucleotides of reads as insertion. For example:

    2-42 16 chr11 86397621 255 23M * 0 0 GTCAACATCAGTCTGATAAGCTA IIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:23 NM:i:0

    Does any one have any idea what happened? What should I do to make it work?

    Thanks,

    Yue
    Last edited by 610617109; 11-17-2015, 11:43 PM.

  • #2
    The 'I's you're seeing are quality scores of your read, not the CIGAR string ...
    'I' in phred-33 qual is 40. Where did you get the read file and how did you perform your alignment ? I think some aligners have to option to ignore quality scores(e.g. treat all quality scores as 40).

    Comment

    Latest Articles

    Collapse

    • 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
    • seqadmin
      The Impact of AI in Genomic Medicine
      by seqadmin



      Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
      02-26-2024, 02:07 PM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 03-14-2024, 06:13 AM
    0 responses
    32 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-08-2024, 08:03 AM
    0 responses
    71 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-07-2024, 08:13 AM
    0 responses
    80 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-06-2024, 09:51 AM
    0 responses
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X