Question: Detecting copy number alterations based on RNA-seq data
1
gravatar for igor
13 months ago by
igor7.0k
United States
igor7.0k wrote:

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

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

cnv rna-seq copy number • 1.4k views
ADD COMMENTlink modified 11 days ago by bhaas110 • written 13 months ago by igor7.0k
3
gravatar for igor
7 months ago by
igor7.0k
United States
igor7.0k wrote:

I just found HoneyBADGER, another method for single-cell RNA-seq:

HoneyBADGER (hidden Markov model integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data) identifies and infers the presence of CNV and LOH events in single cells and reconstructs subclonal architecture using allele and expression information from single-cell RNA-sequencing data.

ADD COMMENTlink written 7 months ago by igor7.0k
1

There is also CONICS:

CONICSmat is an R package that can be used to identify CNVs in single cell RNA-seq data from a gene expression table, without the need of an explicit normal control dataset. CONICSmat works with either full transcript (e.g. Fluidigm C1) or 5'/3' tagged (e.g. 10X Genomics) data.

ADD REPLYlink written 9 weeks ago by igor7.0k
2
gravatar for bhaas
11 days ago by
bhaas110
United States
bhaas110 wrote:

The InferCNV software aims to make the Tirosh & Regev method available as a toolkit:

https://github.com/broadinstitute/inferCNV/wiki

ADD COMMENTlink written 11 days ago by bhaas110
1
gravatar for Chris Miller
13 months ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k 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 13 months ago by Chris Miller20k
1

Is this the paper you are referring to?

ADD REPLYlink written 13 months ago by cbst140
1

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 13 months ago by Chris Miller20k
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