Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Potentially corrupted BAM files

    Hi all,
    I have a question about detecting possible corruptions to BAM files. Essentially, we had a serious hard drive issue and failure across our network. While we have been able to restore our hard drives and retrieve our data, we have noticed issues with many files. for example, in some text files, some information has been changed to non ascii data, or lines deleted from them. We still do not yet know the full extend of the issues but are trying to figure it out. One, potential issue is that we have many 1000's of mapped bam files. We do not know if the files have been corrupted in anyway, and are interested in finding out. One approach (I think) would be to try to convert them back to SAM files, and if it breaks then the file is somehow corrupted. But I was wondering if anyone knew of some other method that can check the file.

    I should note that we do have most of this backed up on a tape storage system that we could go back to, but this would take an exceedingly long time to do for our whole system. So we would like to maybe find the 'bad' files and replace those only. Also, I am not a software engineer, so hopefully this all makes sense

  • #2
    zcat the bam file and check for errors ... example ...

    rfinney@pigdog:~$ file test.bam
    test.bam: gzip compressed data, extra field

    rfinney@pigdog:~$ samtools index test.bam

    rfinney@pigdog:~$ cat test.bam | tr " " "x" > test2.bam # corrupt the file test2.bam

    rfinney@pigdog:~$ samtools index test2.bam
    [E::bam_hdr_read] invalid BAM binary header
    samtools index: "test2.bam" is corrupted or unsorted

    rfinney@pigdog:~$ zcat test.bam > /dev/null

    rfinney@pigdog:~$ zcat test2.bam > /dev/null
    gzip: test2.bam: invalid compressed data--crc error
    gzip: test2.bam: invalid compressed data--length error
    Last edited by Richard Finney; 09-01-2016, 11:46 AM.

    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
    33 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