[miso-users] [help] How to run miso on multiple samples?

[Yarden Katz]

Hi Jerry,

If I understand correctly, you have 4 replicates for the control condition, and 4 for the KO condition.  The question is then how does MISO deal with replicates.  The short answer is that MISO right now only performs pairwise comparisons -- so in this case, you could compare each control with each KO sample, and vice versa.  However, once you generate the summary files and MISO output for each sample, there are several other ways to deal with replicates in general, and the most appropriate one will depend on what downstream analyses you're doing. 

Take a look at Question 13 from the FAQ page in the MISO manual -- it contains some information on this:

http://genes.mit.edu/burgelab/miso/docs/#frequently-asked-questions-faq

Best, --Yarden


On Apr 19, 2012, at 2:03 PM, zhenghui01 at gmail.com wrote:

> Hi All,
> I currently have 4 controls and 4 KO. I ran miso on all those samples, but not sure how should I compare them? I used the following command:
> 
> For controls,
> python run_events_analysis.py --compute-genes-psi hg19/pickled/SE data/control1.bam --output-dir SE/control1/ --read-len 35 --paired-end 250 15
> python run_events_analysis.py --compute-genes-psi hg19/pickled/SE data/control2.bam --output-dir SE/control2/ --read-len 35 --paired-end 250 15 
> python run_events_analysis.py --compute-genes-psi hg19/pickled/SE data/control3.bam --output-dir SE/control3/ --read-len 35 --paired-end 250 15 
> python run_events_analysis.py --compute-genes-psi hg19/pickled/SE data/control4.bam --output-dir SE/control4/ --read-len 35 --paired-end 250 15 
> 
> 
> For KOs,
> python run_events_analysis.py --compute-genes-psi hg19/pickled/SE data/KO1.bam --output-dir SE/KO1/ --read-len 35 --paired-end 250 15
> python run_events_analysis.py --compute-genes-psi hg19/pickled/SE data/KO2.bam --output-dir SE/KO2/ --read-len 35 --paired-end 250 15 
> python run_events_analysis.py --compute-genes-psi hg19/pickled/SE data/KO3.bam --output-dir SE/KO3/ --read-len 35 --paired-end 250 15 
> python run_events_analysis.py --compute-genes-psi hg19/pickled/SE data/KO4.bam --output-dir SE/KO4/ --read-len 35 --paired-end 250 15 
> 
> Then I summarize the miso output for all 8 samples. Now I am not sure how should I compare them to  get differentially expressed isoform? The documentation seemed to give comparison for one sample at each time: python run_miso.py --compare-samples SE/control/ SE/knockdown/ SE/comparisons/. What should I do? Thank you!
> 
> Regards,
> Jerry
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