[miso-users] 0 reads align to all events

[Jian Duke]

Hi Yarden,
I ran MISO with the Tophat output generated by the on-line server Galaxy.
But I got 0 reads align to all events. I have read the FAQ of MISO manual,
but I still do not know what is wrong.
What I did include 1) put the downloaded Tophat output files, both .BAM and
the .BAI files, in the same folder. 2) I indexed SE.mm9.gff (I only carried
out analysis for SE events). Should I process the output files of
Tophat for MISO?
Thanks.
Jian
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