Distinguish Single Cell DNA Sequencing: Human vs Mouse

Question

[ResearchR]

Hey guys,

I have a quick question -

When doing single cell DNA sequencing from human mouse xenograft models - how to confirm via bioinformatic way that the sequence alignment obtained, is from human cell and not mouse cell contamination.

Do you think it is enough to look at sequence alignment statistics ( for example: STAR alignment log file) or is there a specific single cell program available, like "disambiguate" for bulk data?

Cheers, Chris

Answer 1

[h.mon]

You can use bbsplit.sh from the BBMap / BBTools package to split your sequencing into human-ony, mouse-only, ambiguous (aligns to both genomes) and unmapped reads.