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  • Layla
    Member
    • Sep 2008
    • 58
    #1

    All chromosomes and maq

    Hi all,

    Has anybody used hg18.2bit from the ucsc genome browser as the reference genome for MAQ? As I cannot give more than one ref.fa file to MAQ, is this the right way to be aligning solexa reads to the entire human genome?

    Thanks
    Layla
    Tags: None
  • Layla
    Member
    • Sep 2008
    • 58
    #2
    Answering my own question! Not quite sure what the problem with the ucsc hg18 was..but managed to concatenate all the chromosomes into one file, having read a similar query.

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