Hi,

I have PDX RNA-seq data.I want to separate the reads of mouse and human,before comparing with tumor RNA-seq data. Is there any tool to do that?

After removing the mouse reads I want to do differential expression between primary tumors and PDX tumors.

Thanks,  
Ron
[Xenome][1] works pretty well.

 [1]: http://www.ncbi.nlm.nih.gov/pubmed/?term=22689758