MISO comparing two conditions for DEU

[alittleboy]

Hi All,

I am considering using MISO for testing differential exon usage (DEU). I have two conditions, control group and treatment group, each having 3 biological replicates. I read through the manual of MISO, and it seems that it cannot handle biological replicates (cf. DEXSeq properly handles bio. reps and is working well in my situation).

My question is, if I still want to use MISO for DEU, say using

python run_miso.py --compare-samples control/ treatment/ comparisons/

then do I need to somehow "combine" the biological replicates in each group and then do the analysis? I think if that's the option, then I need to merge the BAM files as they are the inputs for MISO:

# Compute Psi values for control sample (BAM file required), using cluster
python run_events_analysis.py --compute-genes-psi mm9/pickled/SE data/control.bam --output-dir SE/control/ --read-len 35 --paired-end 250 15 --use-cluster

There was a related post here, but people didn't mention how to solve the problem.

Thank you so much!!

[alittleboy]

Anyone familiar with this situation with MISO? Please share your thoughts. I really appreciate ;-)