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  • bowtie- paired end - no alignments

    Hi my command for a paired end read is as follows:

    ./bowtie -v 0 -a -p 2 -X 300 hg19 -c -1 TGGGAGATATACCTAATGCTAGATGACCCA, -2 AAGTTTAGGGTACATGTGCAGGTTAGTTA


    and am getting a message that says

    reads that failed to align - 1(100%)

    am not sure if am going wrong with the syntax.it works when I do them as single-end reads.

    help!!
    thanks
    Last edited by madsaan; 06-27-2011, 03:56 PM.

  • #2
    OK.figured it out!!
    Last edited by madsaan; 06-27-2011, 03:57 PM.

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