I am doing RNA seq analyses for patient derived xenografts (human tissues were implanted into mice). Since both human and mouse genomes are highly conserved, it is possible that reads coming from mouse cells accidentally map to the human genome. I am looking for a tool to test reads' distribution over human and mouse genomes. This way, I can eliminate mouse reads which accidentally map to human genome.
I tried "xenome" but it failed to build index (it dies at the sorting step due to time limit). I increased time, RAMs and threads with no better.
I appreciate it if someone could help either fixing xenome or suggesting an alternative tool