Using Miso For Exon-Centric Inference: Combine Bam Files From Replicates?
I plan to use MISO for exon-centric inference and detect differential exon usage between control and treatment samples. There are 3 biological reps in the control, and 3 in the treatment. From the MISO pipeline here, it seems that it cannot deal with biological replicates, i.e. the inputs of MISO are the control.bam and treatment.bam, two single files. My question is, shall I combine (merge) the 3 biological reps in the control group (3 bam files) into a single one (control.bam), and do the same thing for the treatment group (merge 3 into 1), and then analyze? I know this may be sub-optimal, but I cannot see a better solution...
Thank you so much!
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You might take a look at the miso FAQ on the subject:
http://miso.readthedocs.org/en/latest/#answer13
@Sean: Thanks a lot for the link!