Hi, thank you for making SpecImmune!
I've been running this typing using amplicon nanopore data, but I'm finding that several four field alleles are being assigned with 100% confidence, with no one-guess allele being assigned. Here is a screenshot of the formatted final type file:
I'm extracting the code using
/home/asrivastava/SpecImmune/scripts/ExtractReads.sh -s ${sample} -i ${sample}_BAM.bam -g HLA -o reads
and typing with the flags
python3 /home/asrivastava/SpecImmune/scripts/main.py \ -r reads/${sample}.HLA.fastq.gz \ -j 32 \ -i HLA \ -n ${sample} \ -o outs \ --db /home/asrivastava/SpecImmune/db \ -y nanopore \ --seq_tech amplicon
Do I need to be changing settings of the alignment tool to make it more stringent? From the PDF it seems like all these alleles are 100% aligned. Or does this just mean that SpecImmune isn't able to resolve to four fields?
Thank you!
Hi, thank you for making SpecImmune!
I've been running this typing using amplicon nanopore data, but I'm finding that several four field alleles are being assigned with 100% confidence, with no one-guess allele being assigned. Here is a screenshot of the formatted final type file:
I'm extracting the code using
/home/asrivastava/SpecImmune/scripts/ExtractReads.sh -s ${sample} -i ${sample}_BAM.bam -g HLA -o readsand typing with the flags
python3 /home/asrivastava/SpecImmune/scripts/main.py \ -r reads/${sample}.HLA.fastq.gz \ -j 32 \ -i HLA \ -n ${sample} \ -o outs \ --db /home/asrivastava/SpecImmune/db \ -y nanopore \ --seq_tech ampliconDo I need to be changing settings of the alignment tool to make it more stringent? From the PDF it seems like all these alleles are 100% aligned. Or does this just mean that SpecImmune isn't able to resolve to four fields?
Thank you!