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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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No multi-gene mapper #5

Closed Ritabear closed 1 year ago

Ritabear commented 1 year ago

Hello!

I'm trying to run this tool. But, I have some questions about No multi-gene mapper. Could you explain more about No multi-gene mapper? Is it a different mode for the tool?

mourisl commented 1 year ago

I don't think T1K has the warning message about "No multi-gene mapper". Could you please show me the command you used? Thank you.

Ritabear commented 1 year ago

Sorry, I don't explain clearly. I want to know what Fig1a in the paper writing No multi-gene mapper. I find that the program has one line in T1K_manuscript_evaluation: Fig1/Analysis.ipynb, which writes # No multi-gene mapper. Therefore, I assume No multi-gene mapper mean another mode. I am curious about what is No multi-gene mapper and how to use it.

mourisl commented 1 year ago

Thank you for the clarification.

Yes, "No multi-gene mapper" is another mode, where I added the code to ignore the reads mapped to more than one KIR gene. The purpose is to demonstrate that ignoring multi-gene mapped reads is bad. Ignoring multiple gene mapped reads is adopted in several HLA genotypers, such as arcasHLA. It is too hard to modify arcasHLA to work with KIRs, so we add this test to mimic the behavior of arcasHLA. This mode is not really present in T1K.

Just out of curiosity, why do you need this mode?

mourisl commented 1 year ago

If you need this mode, you can comment out the code at https://github.com/mourisl/T1K/blob/master/Genotyper.hpp#L693-L695 .

Ritabear commented 1 year ago

Thank you very much! To be honest, I don't need this mode. However, I saw this mode on the paper and T1K_manuscript_evaluation: Fig1/Analysis.ipynb. Then, I thought No multi-gene mapper was a mode and couldn't find something in the helper message. I can't suppress my curiosity and create an issue. ><

mourisl commented 1 year ago

Haha, then I shall close this issue for now. If you have more questions, please feel free to reopen this one or create a new issue.