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  • yyp777
    Junior Member
    • Aug 2012
    • 2
    #1

    Tophat2 Multiple alignment discrepancy

    Dear All,

    I am trying to get unique sequences when align to hg19 using tophat2.
    When I set parameter "Maximum number of alignments to be allowed" to 1,I got 25% of my data as "multiple alignment" sequences while I got 58%
    when I set the parameter to 20.

    As far as I understand, multiple alignments should be the same since I was using the same data set. Any concern or anyone experience similar results?

    Thanks!

    YYU
    Tags: tophat2 unique sequences
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