How to determine what allele a sample has from FASTQ data?
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2.3 years ago

Hello!

I am interested in a particular gene, HLA-DRB1. I have around 10 samples that I have FASTQ (sequence) data files for. I also have a FASTA file which has all the alleles of HLA-DRB1. It is of this format:

>HLA:HLA01234 HLA-DRB1*1501 1152 bp
ATGGGGCTGGGCCCGGTCTTCCTGCTTCTGGCTGGCATCTTCCCTTTTGCACCTCCGGGA
GCTGCTGCTGAGCCCCACAGTCTTCGTTATAACCTCACGGTGCTGTCCTGGGATGGATCT
GTGCAGTCAGGGTTTCTCACTGAGGTACATCTGGATGGTCAGCCCTTCCTGCGCTGTGAC
AGGCAGAAATGCAGGGCAAAGCCCCAGGGACAGTGGGCAGAAGATGTCCTGGGAAATAAG......


My question is - how can I determine what allele each of my samples has?

Ideally, I'd just like a table that says something like..

sample_id        allele
ID_1             HLA-DRB1*1501
ID_2.            Ambigous


I had a look at a few programs but I'm not sure the best way to approach this.

RNA-Seq sequencing fastq fasta alleles • 491 views