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genomic-medicine-sweden / tomte

A nextflow pipeline for analysing expression and splicing in RNA seq data from rare disease patient
MIT License
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An option to use DNA-seq variants? #162

Open A97paupic opened 1 week ago

A97paupic commented 1 week ago

Description of feature

Hi, I was wondering if you guys have thought to give the pipeline an option to use variants called from a DNA-seq(typically wgs) pipeline to use as input into "ASE read counter" rather than variants called from the RNA-seq itself? I think that would make sense to integrate genomic and transcriptomic data in case both are available.

Thanks for your devoted work, Paul

jemten commented 1 week ago

Hi Paul, yeah that is something that's in the backlog and we definitely want. Using only RNAseq variants we will only be able to catch skewed allelic imbalances but not if expression is entirely missing from one of the alleles. Most often the DNA variants are also available. Thanks for posting so we can keep track of the issue.