0 reads mapped to a single HLA gene

[tequilasunrise0]

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!