Hi, 

I was confronted to the same kind of challenge, but with much smaller organisms (and genomes!). To answer your question, first, you would need the complete genome of your target organism (here: mouse), and then map your reads to this genomes (we used Bowtie2 for that task). Like that, you will map hopefully all sequences from mouse, leaving unmapped all sequences of interest. At the end , mapped sequences. originating from mouse, will be discarded from your dataset.

Hope this suggestion could help you in your work!

Good luck and Merry Christmas!

Vincent

genomes being similar it will be a task to separate the reads ... however give as little mismatches as possible while aligning and it might work :)

This is great challenge to identify the similiar sequence by bioinformatics, the reliable approach is preparing the cleaned samples (labeled by fluorescence and sorted by Flowcytometry) to load for RNA sequencing.

good luck!