Hi, I have RNA-seq data of cancer patients and their matched normal as well. I'd like to calculate for each patient the TMB, but I mostly find information about such calculations for Whole Genome/Whole Exome. Can you advice me what would be the best way to do such calculations? Thanks
You could first call variants using the RNA-seq reads, but this is not ideal - see here: A: Inferring genotype based on RNA sequnces
Kevin
You could check out this approach which seems reasonable (https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-021-00898-y). It would be great to do this in a case where you have TMB from WES for most samples and want to estimate it for the portion that are missing it. You could verify it's accuracy in your data before applying to your missing data. You could use the TMB data you have to tune the results of your missing data. Good luck.
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version 2.3.6
Curiously, their GitHub page (https://github.com/Jessen-Erik/RNA.TOMS) is empty.
Patent? It's always about the money and never about the patient in biotech, but we'll try to convince them otherwise.