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

[zhenghui01@gmail.com]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.mit.edu/mailman/private/miso-users/attachments/20120419/5798f7db/attachment.htm