Tophat2 Multiple alignment discrepancy

yyp777

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Join Date: Aug 2012

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Tophat2 Multiple alignment discrepancy

11-14-2013, 09:50 AM

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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