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
[BBSplit][1] will map the reads simultaneously to multiple references, and output in multiple files, one per reference. Since you're looking at RNA-seq of tumors, you would want to increase the sensitivity over the default, using settings like (if mapping to the genomes):

    bbsplit.sh in=reads.fq ref=hg19.fa,mm10.fa minratio=0.5 maxindel=100000 minhits=1 basename=out_%.fq ambig2=all local

If mapping to transcriptomes, `maxindel=500` would probably be better than `100000`.

 [1]: https://sourceforge.net/projects/bbmap/