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14 months ago
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Dear Community,
I have two omics datasets (WGS and transcriptomics) on tumor/normal cells. I have performed CNV calling on genomics data and DEG on transcriptomics data. Is there any methods/ approach to compare among these two dataset?
Best,
HI jared.andrews07 ,
Thank for your response. That could be a good look at the data.
However, the CNVs are set based on bin size (10kb or 100kb) on reference (whole) genomes, while genes are varying a lot in lengths. For e.g. if a CNVs is defined as 10kb, it would possibly contain several <2kb genes, but only a part of 30kb genes. In addition, a CNVs can possible cover part of the genes, for e.g. start position at 500 of the genes instead of 1 or in front of the gene. As they are not perfect match the position on genomes, I found it difficult to correlate/plot the CNVs vs genes expressions on scatter plot.
How do you think?
A good question, without a perfect answer, but one option is to use something like
cnvkit
'sgenemetrics
command to call absolute copy number for each gene, which attempts to use some sensible defaults to deal with those that span multiple segments:In such cases, one could remove it from the scatter plot (or distinguish it with a different color or shape).
sorry for late response @jared.andrews07,
you did suggest great way to look at this kind of problem and I am working on this with your approach.
Thank a lot,
Best