search

bmvdgeijn / WASP

WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
Apache License 2.0
103 stars 51 forks source link

Is it feasible to use population-level SNP instead of individual sample's variant information? #121

Open zhangjy859 opened 10 months ago

zhangjy859 commented 10 months ago

Hi,

I am trying to count allele specific expression from RNA-seq data, beacuse I am working with specific cell model, I am not have paired SNV infomation, is it feasible to use population-level SNP instead of individual sample's variant information?

Regrads.

Zhang

gmcvicker commented 10 months ago

Hi Zhang, There's not really anyway to do this with the WASP. It is possible to obtain genotypes directly from ATAC-seq or RNA-seq, however, and those genotypes could be used by WASP. E.g. you could try to identify heterozygotes by running GATK haplotype caller on the RNA-seq reads. You could also check out the QuASAR tool by Harvey et al. 2015 (doi: 10.1093/bioinformatics/btu802).

Hope this helps.

zhangjy859 commented 10 months ago

Hi @McVicker

Thank you so much for quick response and useful infomations, but I still have a bit confusing, In fact, I known WASP is a wide known tools and been widely accepted for a long time, I also noticed many works run WASP with common SNP database, for example, dbSNP or 1kg SNP panel (such as He et. al., 2022, https://doi.org/10.1038/s41398-022-01913-1 and Quach et. al., 2016, https://doi.org/10.1016/j.cell.2016.09.024). So despite my reservations about doing so, I was a little surprised when I learned from your answer that such a scheme is not feasible. Is there a mistake in my understanding?

Regrads.

Zhang