Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • AS:i and XS:i SAM File Fields (Bowtie2)

    I've seen posts/advice online stating that multimapper reads can be identified when the AS:i: and XS:i: optional fields in a .SAM file (after alignment with Bowtie2) are equal to one another such as AS:i:5 and XS:i:5 as opposed to the presence of XS:i: alone (which can be added to non-multimapper reads in some instances).

    What are these fields actually describing? The manual for Bowtie2 is quite vague and, for example, simply describes AS:i: as the 'alignment score' - but from where is it derived? What is it specifically describing? And why would it be a multi-mapping read when these fields are equal?

  • #2
    I suggest using required fields for analyses. It's not clear what the AS tag is supposed to report, and the XS tag is custom with no official documentation whatsoever. However, the required MAPQ field is clearly defined; it is the aligner's estimate that the alignment is correct. So, a MAPQ of 3 or lower means the aligner thinks there is a 50% chance or less that the alignment is correct. Uniquely-mapping reads, therefore, will have a MAPQ of 4 or higher.

    Comment


    • #3
      A good explanation of those fields can be found here:



      Basically, AS is the alignment score, and XS is the "suboptimal alignment score", essentially a secondary alignment. If AS and XS are close or equal, then you are getting multiple alignments happening.

      Comment

      Latest Articles

      Collapse

      • 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
      • seqadmin
        Multiomics Techniques Advancing Disease Research
        by seqadmin


        New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

        A major leap in the field has
        ...
        02-08-2024, 06:33 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Today, 06:12 AM
      0 responses
      13 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-23-2024, 04:11 PM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-21-2024, 08:52 AM
      0 responses
      70 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-20-2024, 08:57 AM
      0 responses
      61 views
      0 likes
      Last Post seqadmin  
      Working...
      X