Question: CNV detection of single cell genome sequencing
1
gravatar for Tonny
16 months ago by
Tonny20
Shanghai, China
Tonny20 wrote:

Hi, I have some single cell genome sequencing data and I'd like to know if there is any good solution for CNV detection. I hear that CNVkit is a good choice to detect CNV for bulk data, but I don't google any thing about single cell.

ADD COMMENTlink modified 16 months ago by Eric T.2.3k • written 16 months ago by Tonny20
2
gravatar for Eric T.
16 months ago by
Eric T.2.3k
San Francisco, CA
Eric T.2.3k wrote:

CNVkit should work fine for single cell sequencing data. It doesn't do anything specific to use the single-cell assumption initially, but you can use the cnvkit.pyp call -m clonal command to enforce the assumption that the cells are all identical, with a given ploidy if it's known, otherwise assuming diploid. This is similar to the "quantization" step described by Baslan et al. (above/below).

It's definitely worthwhile to see what else has been developed specifically for single cell data. CNVkit integrates relatively easily with other tools, especially if you are willing to do a little bit of scripting or command-line processing.

ADD COMMENTlink written 16 months ago by Eric T.2.3k

Thank you for your reply.

ADD REPLYlink written 16 months ago by Tonny20
0
gravatar for bernatgel
16 months ago by
bernatgel1.3k
Barcelona, Spain
bernatgel1.3k wrote:

You can take a look at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069701/

They use a custom approach to CNV calling from single cell data but they provide a good guide and access to code as supplemetary material. Not a full blown package, but it might be helpful.

ADD COMMENTlink written 16 months ago by bernatgel1.3k

Thank you for your reply.

ADD REPLYlink written 16 months ago by Tonny20
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