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Old 02-01-2012, 10:40 AM   #1
demis001
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Location: USA

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Question MISO compare two samples with replicate; RNA-SEQ

How can I compare two samples of RNA-SEQ with biological replicate using MISO?

Assuming, I have 10 biological replicates for control and 10 biological replicate for knockdown samples. How can modify the following line to read 10 MISO run under the control directory and 10 MISO run under knockdown directory and compare the two samples with biological replicate?

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

Thanks
DD
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Old 11-17-2012, 07:42 AM   #2
bioliyezhang
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Quote:
Originally Posted by demis001 View Post
How can I compare two samples of RNA-SEQ with biological replicate using MISO?

Assuming, I have 10 biological replicates for control and 10 biological replicate for knockdown samples. How can modify the following line to read 10 MISO run under the control directory and 10 MISO run under knockdown directory and compare the two samples with biological replicate?

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

Thanks
DD
Hi, demis:

I wonder whether you have figured out how to do that? I have the exactly the same question as you. Can you give me some idea if you know how to do it?
Thanks a lot.
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Old 11-19-2012, 12:36 AM   #3
Simon Anders
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Has MISO been updated to now be able to handle biological replicates?

The method presented in the Nature paper could not, which is a very severe limitation and and was one of reasons why we saw a need for a new method and developed DEXSeq (Anders, Reyes, Huber; Genome Res, 2012).
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Old 11-19-2012, 12:04 PM   #4
bioliyezhang
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Quote:
Originally Posted by Simon Anders View Post
Has MISO been updated to now be able to handle biological replicates?

The method presented in the Nature paper could not, which is a very severe limitation and and was one of reasons why we saw a need for a new method and developed DEXSeq (Anders, Reyes, Huber; Genome Res, 2012).
Hi, Simon:

thanks. So far, I think the current version of MISO still does not handle biological replicates. I will try the DEXSeq.
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