Forum:How to deal with contamination in bulkseq samples? Looking at correlated genes?
0
0
Entering edit mode
3 months ago
Seaweed • 0

Hi,

I have run a bulk RNA-seq for 4 tissue samples. Each sample contains 50 cells collected from FACS, but due to technical challenges, my cells of interest account for varying proportions of those 50 cells across the 4 preps. I am wondering if there are any ways to uncover genes that are expressed in my cells of interest even though the samples were a mixture of cell types. My cells are labeled by tdTomato, so I do have counts for tdTomato transcripts. One thought is to find genes that would correlate with tdTomato expression. Is this reasonable? If so, what would be a good way to look for correlated genes in the whole dataset? Clustered heatmap?

Thanks!

RNA-Seq Forum • 149 views
ADD COMMENT

Login before adding your answer.

Traffic: 1394 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6