How to read Cigar Strings in SAM file

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  • Опубліковано 27 сер 2024
  • The ‘CIGAR’ (Compact Idiosyncratic Gapped Alignment Report) string is how the SAM/BAM format represents spliced alignments. Understanding the CIGAR string will help you understand how your query sequence aligns to the reference genome.
    in this video, I hope to you through with you the basic format for the CIGAR strings with a few example. hopefully that would help anyone struggling to understand this format
    Email: liquidbrain.r@gmail.com
    Github: github.com/bra...
    Twitter: / brandon_yeoph

КОМЕНТАРІ • 7

  • @taehoonkim7819
    @taehoonkim7819 5 місяців тому

    Also note that M means either match or mismatch, so that it is compatible with the alignment.

  • @user-cg9iq2hp6j
    @user-cg9iq2hp6j 4 місяці тому

    thanks! really helpful!

  • @irfanalahi380
    @irfanalahi380 3 роки тому +1

    Very helpful. Is there any tool where if I provide a genomic position and a read from a bamfile it will output the corresponding base from the read (not from reference sequence) by parsing the CIGAR string?

    • @user-ef7ih9ww4g
      @user-ef7ih9ww4g 2 роки тому

      Hello, I found it fanxingguo.blogspot.com/2022/08/test.html

  • @subodhgaikwad3366
    @subodhgaikwad3366 2 роки тому

    Thanks !

  • @Sun48100
    @Sun48100 3 роки тому

    This is helpful but what about character H and X?

    • @LiquidBrain
      @LiquidBrain  3 роки тому

      You can get a detail explanation of the string here:
      www.drive5.com/usearch/manual/cigar.html