Question: Distinguish Single Cell DNA Sequencing: Human vs Mouse
0
gravatar for ResearchR
6 months ago by
ResearchR50
ResearchR50 wrote:

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

ADD COMMENTlink modified 6 months ago by h.mon24k • written 6 months ago by ResearchR50
2
gravatar for h.mon
6 months ago by
h.mon24k
Brazil
h.mon24k wrote:

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.

ADD COMMENTlink written 6 months ago by h.mon24k
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