Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Mapping possition in SAM format

    Hi all,
    I have question concerning the SAM format. I need to define position of read mapped to the reference. Which means position of first base of the read regardless if matched or not to reference. I know there is field POS in SAM format but it refers to position of the first matched base.

    example:
    reference-AGCATGTTAGATAAGTGTCTAGGATCATATGCATGA
    mapped read--TAGTTAGATAAGTGT

    using this example POS is 6 - the first matched base is G on the 6th position of the reference
    however I need to get 4 because T is the aligned with 4th position

    Do you have any idea how to get this information from SAM format?

    cheers

    Roman

  • #2
    If the position is 6, then the first two bases were soft-clipped and the CIGAR string starts with 2S. You can, thus, parse the CIGAR string and modify the start position as appropriate. There are some functions in the pysam module that can help with this, should that be useful for you.

    Comment


    • #3
      Originally posted by dpryan View Post
      If the position is 6, then the first two bases were soft-clipped and the CIGAR string starts with 2S. You can, thus, parse the CIGAR string and modify the start position as appropriate. There are some functions in the pysam module that can help with this, should that be useful for you.
      Great, I piped couple of awk commands and it works perfectly. Thanks for saving my time

      Roman

      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
      34 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-08-2024, 08:03 AM
      0 responses
      72 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-07-2024, 08:13 AM
      0 responses
      81 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