Question: Distinguish Single Cell DNA Sequencing: Human vs Mouse
0
gravatar for ResearchR
2.2 years ago by
ResearchR80
ResearchR80 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 2.2 years ago by h.mon31k • written 2.2 years ago by ResearchR80
2
gravatar for h.mon
2.2 years ago by
h.mon31k
Brazil
h.mon31k 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 2.2 years ago by h.mon31k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1867 users visited in the last hour