HLA typing for samples with multiple SRRs

[OrielResearchCure]

Hello,

When using RNA-seq from the GEO dataset, there are cases where the RNA-seq has multiple SRR files (per run). Each one of the SRR files has fastq files mapped to it.
What will be the right way to use these files for HLA typing?
Should I concatenate the FASTQ files and then run the arcasHLA on the combines fastq file or can i run the arcasHLA on each one of the SRRs’ FASTQ files and combine the genotype results?

Thanks,
Eila