Does HLAminer work for the Nanopore RNA-seq data?

[wt2015-github]

If yes, which pl script is the best one? Thanks!

[warrenlr]

We provided an initial solution for WGS nanopore reads 3 years ago, it is documented here, with example command/script:

https://github.com/bcgsc/HLAminer#predicting-from-nanopore-reads-

It's not fully tested, however, so use caution in interpreting its output/predictions.

It should be possible to adapt the commands to work with RNA-Seq reads instead. You could run something like:

HPRArnaseq_ONTclassI-IIdemo.sh myRNAseqONT.fa.gz

This script is now in the distribution, & after fetching http://www.bcgsc.ca/downloads/btl/hlaminer/GCA_000001405.15_GRCh38_genomic.chr-only-noChr6-HLA-I_II_CDS.fa.gz and updating the ../database/HLA-I_II_CDS.fasta file (execute the update bash scripts in the database folder), it should run (see bash script below). Again, I urge caution in interpreting the output, as it has NOT been tested. Good luck!

HPRArnaseq_ONTclassI-IIdemo.sh :

#!/bin/bash

if [ $# -ne 1 ]; then
        echo "Usage: $(basename $0) <NANOPORE RNA-seq FASTA/FASTQ (gzip or not)>"
        exit 1
fi

echo "Predicting HLA from $1 RNA-seq ONT reads..."
echo "Fetching database for alignment..."
wget http://www.bcgsc.ca/downloads/btl/hlaminer/GCA_000001405.15_GRCh38_genomic.chr-only-noChr6-HLA-I_II_CDS.fa.gz
####
echo "Running minimap2 (minimap2-2.12-r827) and HLAminer v1.4 combined ..."
/usr/bin/time -v -o minimap_hlaminerRNASEQont_CDS.time minimap2 -t 60 -ax map-ont --MD GCA_000001405.15_GRCh38_genomic.chr-only-noChr6-HLA-I_II_CDS.fa.gz $1 | ../bin/HLAminer.pl -h ../database/HLA-I_II_CDS.fasta -s 500 -q 1 -i 1 -p ../database/hla_nom_p.txt -a stream
mv HLAminer_HPRA.csv HLAminer_HPRA_$1.csv
mv HLAminer_HPRA.log HLAminer_HPRA_$1.log

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