Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • bwa reporting of multi-mapped reads

    I am mapping some RNA-seq data with bwa and would like to do some analysis on where multi-mapped reads fall.

    I know that I can extract multi-mapped reads by looking for mapq < 23 and/or the XA flag on the reads. However, I am wondering how bwa decides which location to report for a read that can be mapped to two different locations equally well. Does it choose a random one? Does it always report the first one? Something else?

    Does anybody know what exactly bwa does here?

  • #2
    There is a command line argument: -R. If BWA reach this limit, stop searching further locations.

    Comment


    • #3
      I don't think this answers my question. I want to know how bwa decides which of the location it reports as the primary alignment.

      Comment


      • #4
        Its a random choice. Also when there are more than 1 equally "best" hits for a read the alignment gets a MAPQ of 0. When the author benchmarks the BWA tools he usually throws out alignments with MAPQ = 0 since those are random assignments.
        Last edited by sdriscoll; 02-14-2014, 11:39 PM.
        /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
        Salk Institute for Biological Studies, La Jolla, CA, USA */

        Comment


        • #5
          Great, thank you!

          Comment


          • #6
            Originally posted by sdriscoll View Post
            Its a random choice. Also when there are more than 1 equally "best" hits for a read the alignment gets a MAPQ of 0. When the author benchmarks the BWA tools he usually throws out alignments with MAPQ = 0 since those are random assignments.
            This is not correct - if there are two equal-scoring locations, bwa gives both a mapping score of 3 (equivalent to 50% probability), and so forth.

            If you want to map RNA-seq data for organisms with splicing, such as eukaryotes, bwa is not the right tool. You should use a splice-aware aligner like Tophat or BBMap.

            Comment


            • #7
              what about duplicate how BWA deals with duplicate , and Is it possible to give me the source of this info.

              Comment


              • #8
                [QUOTE=Brian Bushnell;134401]This is not correct - if there are two equal-scoring locations, bwa gives both a mapping score of 3 (equivalent to 50% probability), and so forth.

                what about duplicate how BWA deals with duplicate , and Is it possible to give me the source of this info.

                Comment

                Latest Articles

                Collapse

                • seqadmin
                  Essential Discoveries and Tools in Epitranscriptomics
                  by seqadmin


                  The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...
                  Today, 07:01 AM
                • seqadmin
                  Current Approaches to Protein Sequencing
                  by seqadmin


                  Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
                  04-04-2024, 04:25 PM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, 04-11-2024, 12:08 PM
                0 responses
                37 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 04-10-2024, 10:19 PM
                0 responses
                39 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 04-10-2024, 09:21 AM
                0 responses
                35 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 04-04-2024, 09:00 AM
                0 responses
                54 views
                0 likes
                Last Post seqadmin  
                Working...
                X