Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Why does samtools idxstats not show the stats

    The ref sequences in my bam file are 1, 2, ...

    idxstats reports get that 0 reads are mapped to each reference.

    Code:
    $ samtools idxstats MyBam.bam
    1	197195432	0	0
    10	129993255	0	0
    11	121843856	0	0
    And yet, the bam file is fine, I can see millions of reads mapped to each reference sequence (with samtools view) and I can run mpileup on it as well. Why would idxstats not work? Any ideas?

    Thanks,
    Gulu
    Kamalakar Gulukota,
    Director,
    Center for Bioinformatics and Computational Biology
    NorthShore University Health System, [email protected]

  • #2
    I'm not sure why it wouldn't work - I never had a problem with it before.

    If you're looking for a workaround you could so something like:
    Code:
    samtools view MyBam.bam | cut -f3 | sort | uniq -c
    Though this will omit the length of the reference.

    I hope this helps!

    Comment


    • #3
      Thank you twaddlac! Yes, I have been doing something like that. Unfortunately I have multiple files and each file has billions of lines and hence my server takes hours per file for this. I thought idxstats might have a fast way. Oh well ...
      Kamalakar Gulukota,
      Director,
      Center for Bioinformatics and Computational Biology
      NorthShore University Health System, [email protected]

      Comment


      • #4
        Try reindexing - 'samtools idxstats' relies on extra fields in the BAI file which are not present in very old BAI files (early versions of 'samtools index' didn't write them).

        Comment


        • #5
          Thank you maubp!

          I reindexed and it worked fine. (The original .bai file was something I downloaded from a public site along with the bam file).
          Kamalakar Gulukota,
          Director,
          Center for Bioinformatics and Computational Biology
          NorthShore University Health System, [email protected]

          Comment


          • #6
            Originally posted by kgulukota View Post
            Thank you maubp!

            I reindexed and it worked fine. (The original .bai file was something I downloaded from a public site along with the bam file).
            Great - can you try contacting the site so they can update their BAI files too?

            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...
              04-22-2024, 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, Yesterday, 08:47 AM
            0 responses
            12 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-11-2024, 12:08 PM
            0 responses
            60 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 10:19 PM
            0 responses
            59 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 09:21 AM
            0 responses
            54 views
            0 likes
            Last Post seqadmin  
            Working...
            X