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bcgsc / HLAminer

⛏ HLA predictions from NGS shotgun data
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What is the purpose of patient.fof? #30

Closed WQ0829 closed 1 year ago

WQ0829 commented 1 year ago

Hi, I tried using my .fastq files and wrote the full path in the patient.fof. While I was trying to run HPRAwgs_ONTclassI-IIdemo.sh, it seemed like it is using ERR2585115.fastq.gz instead of my files. Is there a specific place where I should specify to use files in patient.fof?

warrenlr commented 1 year ago

patient.fof is only used in conjunction with HLAminer HLA predictions from targeted short read assembly.

Please note that the bash script HPRAwgs_ONTclassI-IIdemo.sh is simply a demo script, to test the streaming functionality.

I encourage you to take a look at the preprint for info on how to run on your data. But essentially, you simply need to replace the ERR2585115.fastq.gz in this command:

/usr/bin/time -v -o minimap_hlaminerERR2585115-1mod.time minimap2 -t 60 -ax map-ont --MD ../database/GCA_000001405.15_GRCh38_genomic.chr-only-noChr6-HLA-I_II_GEN.fa.gz ERR2585115.fastq.gz | ./HLAminer.pl -h ../database/HLA-I_II_GEN.fasta -s 500 -q 1 -i 1 -p ../database/hla_nom_p.txt -a stream

thank you for your interest in HLAminer

github-actions[bot] commented 1 year ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your interest in HLAminer!