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
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