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

[xfliwz]

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!