Hi,
I am analyzing genomic (RNA-seq) data from Patient Derived Xenograft tumor samples where cancer patient tumors are transplanted and grown in a mouse, harvested, and then extracted DNA and RNA is sequenced.  I have never done this before and wondering if human or mouse reference genome should be used.  I would guess the human reference genome should be used for alignment but is it possible that there would be some mixed in mouse cells?
Thanks,
- Pankaj
Hi,
you would use human reference for alignment of course. 

There are some methods to remove possible contaminated reads originating from mouse cells. You can use uniquely mapped reads with high mapping quality. There is also a [tool][1] available to separate reads especially from xenograft samples.


  [1]: http://bioinformatics.oxfordjournals.org/content/28/12/i172.full