[miso-users] Question about running MISO with TopHat

[Lin, Kuan-Ting]

Dear MISO users,

I am trying to run MISO on my TopHat (version 2.0.14) files, but couldn’t get any results. It kept returning the following message:

Loading BAM filename from: input.sorted.bam
Filtered out 1 read pairs that were on same strand.
Filtered out 1 reads that had no paired mate.
  - Total read pairs: 0
No. reads discarded due to strand violation: 0
Only 0 reads in gene, skipping (needed >= 20 reads)
Computing Psi for 1 genes...
  - 6:144385735:144385588|144385605:- at 6:144290044:144290115:-
  - GFF filename: index/miso/hg19/chr6/6:144385735:144385588|144385605:- at 6:144290044:144290115:-.pickle
  - BAM: input.sorted.bam
  - Outputting to: MISOtest
  - Paired-end mode:  (200.0, 15.0)

It appears that MISO couldn’t extract reads from my bam file.

Could someone help?

Thanks,
Woody