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0 reads mapped to a single HLA gene #119

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tequilasunrise0 opened this issue Feb 1, 2024 · 0 comments

tequilasunrise0 commented Feb 1, 2024

Thanks for developing the tool!

I have Smart Seq 2 data. I've tried either fastq files or bam file as input, but it always give me such result:

[alignment] Processed 29558126 reads, 0 pseudoaligned to HLA reference
[alignment] 0 reads mapped to a single HLA gene

Many valid reads, but 0 mapped to HLA. How can I solve this?

Very appreciate!

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