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  • #1

    SAMtools reports error when converting Tophat's result

    Dear SEQanswers fellows, I had a problem of outputting result of Tophat. I've searched this forum and googled to find a answer but nothing I can use to solve this problem.

    I got an error message when Tophat almost finished an analysis of 100M tags of a SOLiD 50SE RNA-seq.

    The error message was:
    Parse error at line 23113384: sequence and quality are inconsistent

    I tried to convert the accepted_hits.sam to BAM by SAMtool command but the error showed again.

    My software environment is:
    Ubuntu 10.10
    Bowtie 0.12.7
    Tophat 1.1.4
    SAMtools 1.11

    Could someone give me a clue of what's happened?

    Thank you very much.


    Jack
    Tags: None
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