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roland-rad-lab / MoCaSeq

Analysis pipelines for cancer genome sequencing in mice.
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CNV #13

Closed nilesh-iiita closed 2 years ago

nilesh-iiita commented 2 years ago

Unable to access copy number variation results.

NikdAK commented 2 years ago

Could you please provide us more information about the issue? Are the BAM files or other files created?

There is a log file located here where you can extract more details about your issue: QC/samplename.report

nilesh-iiita commented 2 years ago

Thanks for the reply, I figured it out. The CNV data is in the Copywriter.genes.Mode.txt file. Though I did not how Mean values are calculated. Would you please briefly explain?

NikdAK commented 2 years ago

The value for each gene is taken as the average of all overlapping segments (should in most cases be just 1 segment).

The copynumber value ("Mean" of all copy ratios) is calculated using Copywriter: https://pubmed.ncbi.nlm.nih.gov/25887352/ https://github.com/PeeperLab/CopywriteR