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  • Extracting readnames from pindel

    Hi everybody, very short question:

    Is there a possibility to get the 'mapped' readnames from pindel?
    In that way, one could extract those reads from the unmapped-read pool.

  • #2
    Originally posted by robinweide View Post
    Hi everybody, very short question:

    Is there a possibility to get the 'mapped' readnames from pindel?
    In that way, one could extract those reads from the unmapped-read pool.
    in the Pindel raw output, read names are displayed for each read with split-read alignment. the string start with @ is read name.

    let me know if you have any questions.

    Kai

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    • #3
      Ah okay, didn't scrolled all the way to the right of your example output.

      Another question: the CloseEndMapped- file... Are those the (former unmapped) reads, that are now split-mapped? And what about the RP-file?

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