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  • De-Multiplexing MiSeq Data

    Hi,

    I have 3 fastq files consisting of R1, R2 read files and
    a separate index file. for example They are in the format below.

    R1: @M00132:6:000000000-A0JG4:1:1:18014:1842 1:N:0:0
    Sequence data

    R2: @M00132:6:000000000-A0JG4:1:1:18014:1842 2:N:0:0
    Sequence data

    Index: @M00132:6:000000000-A0JG4:1:1:18014:1842 1:N:0:0
    CTCGGT
    +
    <@@DFD

    I want to split the R1 and R2 files based on this barcode.
    and create new files that contain these barcodes

    does any script or tool avaliable online so that i can work on it?

  • #2
    Check post #7 in this thread: http://seqanswers.com/forums/showthread.php?t=22407 There is a script there that you may need to tweak for your files.

    FYI: As you create a new thread SeqAnswers does an automatic search on your post and then suggests past threads that may help. Look for them in the "Similar Threads" section at the top.

    I am still baffled as to why sequencing facilities hand out sequence data without completing the de-multiplexing.
    Last edited by GenoMax; 11-08-2012, 12:00 PM.

    Comment


    • #3
      Originally posted by GenoMax View Post
      I am still baffled as to why sequencing facilities hand out sequence data without completing the de-multiplexing.
      Maybe he should just ask. Sometimes customers don't mention anything about indices ... bad luck if these samples are put on a SE run. But as PE runs are much more frequent nowadays (at least in our environment), it shouldn't be much of a problem.

      my 2p :-)

      Comment

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