[miso-users] bayes factor calculation not consistent among replicates

[Gao, James (NIH/NCI) [E]]

Hi Yarden,

I am comparing alternative splicing events in a pair of control/treatment
samples. Each has two replicates. If I looked at the junction reads in
UCSC genome browser, the two replicates look similar and one exon is
clearly spliced differently between control and treatment. However, only
replicate #1 comparison generated a bayes factor, not replicate #2. I
looked at the miso calculation, it seems there are no .miso files created
for the 2nd replicates for that particular exon junction. Not quite sure
what controls the generation of .miso files.

Another non-related question about sashimi-plot, how the # of exon
junction reads are decided? They seem to be different from the
junctions.bed file that TopHat generated.

Thank you.

James