[miso-users] 0 reads align to all events

[Yarden Katz]

Hi Jian,

I use MISO on Tophat output regularly so it should not require pre-processing.  Are you sure that your Tophat BAMs match the headers (i.e. chromosomes names) of SE.mm9.gff?  I.e. if you do:

samtools view yourbam.bam | head

Do the alignments align to a "chr*" style chromosome?  

Also, is your --read-len argument correct?  MISO needs to be given the right read length argument.  If your reads are 50bp and you feed it a different number in --read-len, it will not work.

 --Yarden


On Jan 14, 2013, at 9:57 PM, Jian Duke wrote:

> 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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