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  • 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

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