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  • fenguita
    Junior Member
    • May 2012
    • 1
    #1

    Alignment of reads in REPETITIVE regions

    Hi All

    I am dealing with a smallRNA seq dataset from Ilumina machines in patients that showed trinucleotide expansions in some genes. Since this is a repetitive region that could be matched elsewhere in the genome, how can I deal with that ?.

    I am using Bowtie for alingning the reads. When I use a very astringent approach (-m 1), I got no reads aligned with my region...

    Any of you is dealing with something like that. Any suggestions for more specialized software do circunvent these problems ?

    All the best and thanks in advance

    Paco
    Tags: None
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