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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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Multiple paired-end fastq files for the same sample #35

Open Bondada20 opened 1 month ago

Bondada20 commented 1 month ago

Hello,

Thanks for this amazing tool.

Any recommendation on the best approach to take when one has multiple paired-end fastq files for the same sample? An example is the 1000 genome 30X WGS files (see attached PNG). I want to infer the HLA types on the WGS data from the 1000 genome project. Screenshot 2024-07-20 050648

mourisl commented 1 month ago

You can use wildcard in the file name. For example, "-1 ERR_1.fastq.gz -2 ERR_2.fastq.gz" here. It might be better to use all the reads from the sample.

Bondada20 commented 1 month ago

Thanks!

I ran run-t1k on one of the paired files and the inferred hla type results were the same when compared to the published sanger sequencing results. But as you said, I will use all the reads from the sample. This might be a lot slower compared to using just one pair (the largest in terms of file size).