RNA expression quantification quality for DRB3/4/5

mourisl / T1K

T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with bulk or single-cell RNA-seq, WGS or WES data.

MIT License

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RNA expression quantification quality for DRB3/4/5 #19

Closed lucy-tian closed 10 months ago

lucy-tian commented 10 months ago

Hi,

I wanted to ask if you recommend T1K for DRB3/4/5 RNA expression quantification at the 4 digits level. If I understand corrrectly, you're using reference data for the alleles from IPD-IMGT/HLA database (2021)? Would you recommend building custom databases using the most up-to-date references from IPD-IMGT/HLA?

mourisl commented 10 months ago

We did not fully test the DRB3/4/5 as they lack ground truths in real data sets, but based on the abundances estimations, I think 4 digits should be fine.

You can always use the "t1k-build.pl" to pull down the newest IP-IMGT/HLA version, and a recent processed HLA reference for T1K is at https://github.com/mourisl/T1K/releases/tag/v1.0.4 .

Hope these help.

lucy-tian commented 10 months ago

Thank you!