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  • dan
    wiki wiki
    • Jul 2008
    • 194
    #1

    Challenging read mapping problem

    Hi,

    I have about 70Gbp of paired-end data from potato [1] that I'd like to map to one of the chromosomes (chr04). I only want pairs where one end or the other, or both, matches chr04.

    Aside from the scale of the problem, the format of the files is a pain, because each pair is in a different file.

    Any tips on how to do this (efficiently)?

    A prize goes to the best answer ;-)


    Cheers,
    Dan.

    [1] http://www.ebi.ac.uk/ena/data/view/SRA029323
    Last edited by dan; 09-18-2012, 09:09 AM. Reason: Either end or both ends can match, and I want to return the pair.
    Homepage: Dan Bolser
    MetaBase the database of biological databases.
    Tags: fastq, illumina reads, paired end, read mapping, short read alignment
    • TiborNagy
      Senior Member
      • Mar 2010
      • 329
      #2
      Most of the aligners handle paired data in different files. I do not think it is a problem. Use BWA or other aligner program.

        Comment

        • dan
          wiki wiki
          • Jul 2008
          • 194
          #3
          Yup, bowtie worked fine.
          Homepage: Dan Bolser
          MetaBase the database of biological databases.

            Comment

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