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  • 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

  • #2
    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.

    Comment


    • #3
      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).

      Comment


      • #4
        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.

        Comment

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