Entering edit mode
6.7 years ago
reui879
▴
10
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
