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  • Editing SAM files

    Dear all,

    I want to remove reads that map to ribosomal RNAs. I tried to modify the sam file (output of TopHat), and remove the reads that correspond to rRNAs. However, I could not run cufflinks on the modified sam files. Then I tried to sort them by converting them to bam (using samtools), but even then, it still did not work. I got the following error messages from cuffdiff.

    [22:39:41] Inspecting maps and determining fragment length distributions.
    SAM error on line 66185: CIGAR op has zero length
    SAM error on line 94994: CIGAR op has zero length
    SAM error on line 135374: CIGAR op has zero length

    Has anyone seen this error? What does it mean?

    What would you recommend to remove ribosomal reads?

    thanks,
    Grace

  • #2
    How did you removed the reads from SAM which correspond to rRNA?

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    • #3
      I just looked at the coordinates of each SAM output, and removed lines that overlapped with rRNA locations, as I read in each line.

      I reasoned that since my SAM file was sorted before editing, it should have remained sorted if I just moved certain lines.

      Comment


      • #4
        Regarding the error message you got, there is some discussion at:http://seqanswers.com/forums/showthread.php?t=3551
        If you moving out the reads (from sam file) corresponding to rRNA, you can remove them from your original fastq file (using read IDs) and then re-run the alignment.

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