Closed kwanghoon821 closed 3 years ago
hello, thanks for your message and interest in HLAminer.
Predictions only appear in the csv file if they meet the minimum thresholds:
prompt> ./HLAminer.pl
Usage: ./HLAminer.pl [v1.4]
-i minimum % sequence identity...............<99>
-q minimum log10 (phred-like) expect value...<30>
-s minimum score.............................<1000>
The log will track everything. You may wish to lower the above thresholds to see predictions in the csv, but at the risk of a lower confidence in predictions.
Lastly, know that WES isn't the typical use-case for HLAminer, as certain HLA alleles may not be picked up by exon capture probes.
good luck!
hello, thanks for your message and interest in HLAminer.
Predictions only appear in the csv file if they meet the minimum thresholds:
prompt> ./HLAminer.pl Usage: ./HLAminer.pl [v1.4] -i minimum % sequence identity...............<99> -q minimum log10 (phred-like) expect value...<30> -s minimum score.............................<1000>
The log will track everything. You may wish to lower the above thresholds to see predictions in the csv, but at the risk of a lower confidence in predictions.
Lastly, know that WES isn't the typical use-case for HLAminer, as certain HLA alleles may not be picked up by exon capture probes.
good luck!
Wow, thank you for quick and nice advice.
I will do your advice!
Hi, I used HLAminer for the first time using WES data generated from FFPE sample.
Can you check my command and results?
This is for alignment bwa mem -t 20 -M path/to/database_bwamem/HLA-I_II_CDS.fasta A_1.fastq.gz A_2.fastq.gz > HLAminer_A.sam
This is for typing path/to/HLAminer.pl -a HLAminer_A.sam \ -h path/to/database_bwamem/HLA-I_II_CDS.fasta \ -p path/to/database/hla_nom_p.txt \ -l A_result
And this is results in csv file. No result for HLA-A,B,C,E
HLA-F Prediction #1 - F01 | | F01:01:03:01 | 2413.96 | 7.78E-17 | 161.1 F*01:01P | 1614.99 | 1.82E-11 | 107.4
HLA-G Prediction #1 - G01 | G01:01P | 1614 | 2.56E-14 | 135.9 G*01:04P | 1008 | 3.20E-09 | 84.9
Log file has results of HLA-A,B,C,E. Should I see log file?
Thank you!