Question: HLAminer problem with output file
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gravatar for reui879
3.6 years ago by
reui87910
reui87910 wrote:

I have two different sets of WGS breast cancer data from two different experiments and am trying to run them through HLAminer to get the HLA alleles. I am using the exact same commands for both sets of data but only one dataset is giving me the alleles in the output .csv file. These are the commands I am using. I tried using Bowtie2 instead of BWA but it didn't work. Does anyone know how to fix this? Thanks!

bwa aln /opt/compsci/HLAminer/1.3.1/database/HLA_ABC_GEN.fasta /fastscratch/projects/dna_vinod_1.fastq /projects/mclauk/tum_dir/dna_vinod_1.fastq_tumDNA_neoantigens/dna_vinod_1.fastq_.sai  

bwa aln /opt/compsci/HLAminer/1.3.1/database/HLA_ABC_GEN.fasta /fastscratch/projects/dna_vinod_2.fastq /projects/mclauk/tum_dir/dna_vinod_1.fastq_tumDNA_neoantigens/dna_vinod_1.fastq_.sai  

bwa sampe /opt/compsci/HLAminer/1.3.1/database/HLA_ABC_GEN.fasta /projects/mclauk/tum_dir/dna_vinod_1.fastq_tumDNA_neoantigens/dna_vinod_1.fastq_.sai /projects/mclauk/tum_dir/dna_vinod_1.fastq_tumDNA_neoantigens/dna_vinod_1.fastq_.sai /fastscratch/projects/dna_vinod_1.fastq /fastscratch/projects/dna_vinod_2.fastq /projects/mclauk/tum_dir/dna_vinod_1.fastq_tumDNA_neoantigens/dna_vinod_1.fastq_.sam  

HLAminer.pl -a /projects/mclauk/tum_dir/dna_vinod_1.fastq_tumDNA_neoantigens/dna_vinod_1.fastq_.sam -h /opt/compsci/HLAminer/1.3.1/database/HLA_ABC_GEN.fasta -p /opt/compsci/HLAminer/1.3.1/database/hla_nom_p.txt
software error • 994 views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by reui87910
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