Open Bondada20 opened 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.
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).
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](https://github.com/user-attachments/assets/e971792d-511b-4117-84dc-03df07310172)