Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Non-ascii characters in bam file causes htseq-count error

    Hello everybody,

    I have aligned bam files (using STAR version 2.6.1a_08-27) and want to quantify them using htseq-count (version 0.9.1). When I run htseq-count, some bams run through perfectly fine, but for some I get following error:

    >>>
    ....
    13300000 SAM alignment record pairs processed.
    13400000 SAM alignment record pairs processed.
    Error occured when processing SAM input (record #26816395 in file /data/folder/file.bam):
    'ascii' codec can't decode byte 0xe4 in position 4: ordinal not in range(128)
    [Exception type: UnicodeDecodeError, raised in libcutils.pyx:134]
    >>>

    When I go back to the bam file, this specific line (26816395) contains a question mark in the quality part of the read (either ? or ^?). I used to deal with this by just removing this line since it were only one or a few reads per file; but now I have at least 30 lines or more with question marks, so I don't just want to remove all the reads.
    The problem is that the character is not REALLY a question mark (I know this because when i try to grep for '?', nothing comes up). This means that it is just a substitution for an unknown character.


    So my question is: how do I remove non-ascii characters in the bam file?
    (alternatively: does somebody know where they come from in the first place? Can I redo the alignment using different parameters?)


    I've been trying to find a solution for quite some time and I appreciate any help or work around

    Thanks!

  • #2
    Cross-posted (and has a possible answer): https://www.biostars.org/p/402237/

    Comment


    • #3
      Hi GenoMax!
      Thanks for pointing this out, I posted the question here yesterday, but I didn't see it online nor did I get a mail that is was in the process of posting/ under review or anything similar. I figured it was a problem so that's why I posted it again on Biostars

      Sorry! I will delete it here.
      Thanks


      .....
      edit: how does one delete a thread?
      Last edited by loui_; 10-10-2019, 04:42 AM.

      Comment


      • #4
        No need to delete. If someone finds this thread by search they will know where to get the answer.

        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
        32 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-08-2024, 08:03 AM
        0 responses
        71 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-07-2024, 08:13 AM
        0 responses
        80 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