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  • How to identify diff from RNA-seq data set with DNA pollution

    Hi all,

    I have two RNA-seq data sets of two mouse sample respectively. For the expriment error, there may be DNA reads in those data sets. I find the percentage of chrM reads is 13% (VS another RNA-seq data < 5% chrM). So, my questions are like follows:

    1, What is the proper percentage of chrM reads in normal RNA-seq data set of mouse or human?
    2, How to identify the differentially expressed genes from the DNA polluted RNA-seq data set (it is not possible for me to redo RNA-seq with few sample)?



    Thanks for your attention!
    Last edited by xfliwz; 01-10-2013, 12:04 AM.
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