Question: CNV detection from RNA-seq data
0
gravatar for igor
11 weeks ago by
igor4.9k
United States
igor4.9k wrote:

I've seen a few papers use RNA-seq data to detect copy number info. However, it's always using "custom scripts" in my experience. Is there a publicly available tool for doing that?

I found inferCNV, but that is designed for single-cell data which will have a very different profile from bulk RNA-seq.

rna-seq • 215 views
ADD COMMENTlink modified 11 weeks ago by Chris Miller19k • written 11 weeks ago by igor4.9k
1
gravatar for Chris Miller
11 weeks ago by
Chris Miller19k
Washington University in St. Louis, MO
Chris Miller19k wrote:

To my amazement, Aviv Regev's lab did it, but I cannot find the paper at the moment (please link it here if you find it!). Suffice to say, it's a complex process, and one which produces only very rough outlines of the CN landscape. You will probably only pick up very large events (multi-Mb), and it will likely depend on having a large cohort with which to average out the noise inherent in expression.

ADD COMMENTlink written 11 weeks ago by Chris Miller19k

Is this the paper you are referring to?

ADD REPLYlink written 11 weeks ago by chloe.steen120

Yeah, I saw Aviv talk at a conference, but that seems like the right paper. Even more flabbergasted that it works with single-cell RNAseq. Amazing stuff!

ADD REPLYlink written 11 weeks ago by Chris Miller19k
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