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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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Providing candidate fq files as input #4

Closed moutsian closed 1 year ago

moutsian commented 1 year ago

Hi,

When starting genotyping from stage 1 or stage2, the program is looking for the candidate fq files by trying to infer the name from the output directory and prefix. It would be useful to be able to specify where these candidate fq files are as an input argument instead, so that the outputs could be saved in different directories (e.g. for when testing different cov/frac options).

I think there is currently no such input option? Apologies if I've missed it.

Cheers, Loukas

mourisl commented 1 year ago

Could you please try the "--noExtraction" option? Then it should directly use the candidate fq files in other directories.

moutsian commented 1 year ago

Thank you very much for the rapid response! I used the --noExtraction option and specified candidate reads fq files with -1 and -2 and it works fine indeed.

Cheers, Loukas