Hello author,
I have some data on RNAseq and I know that some of these samples are HLA02 positive (tested using flow cytometry), but I only know that one of the chromosomes is like this(HLA02 positive) and the other chromosome HLA subtype is unknown. It's just that I used arcasHLA to test the HLA of these samples and found that there was no HLA02 at all in the A subtype A in the arcasHLA test results, but using another software, optitype, I could correctly predict that there was HLA02. This confuses me and wonders if there is anything wrong with my operation?
The original bam file is generated from the histat2
Hello author, I have some data on RNAseq and I know that some of these samples are HLA02 positive (tested using flow cytometry), but I only know that one of the chromosomes is like this(HLA02 positive) and the other chromosome HLA subtype is unknown. It's just that I used arcasHLA to test the HLA of these samples and found that there was no HLA02 at all in the A subtype A in the arcasHLA test results, but using another software, optitype, I could correctly predict that there was HLA02. This confuses me and wonders if there is anything wrong with my operation?
The original bam file is generated from the histat2
the IMGTHLA is the latest version
then ./arcasHLA extract *.bam -o . -t 8 -v
then
arcasHLA genotype 1.fq.gz 2.fq.gz -g A,B,C,DPB1,DQB1,DQA1,DRB1 -G ~/data2/Immu_age/arcasHLA/test/output/test.genotype.json -o . -t 8 -v
the result of arcasHLA(one sample) A": ["A11:173", "A01:01:01"], "B": ["B39:39:01", "B07:02:01"], "C": ["C07:50", "C01:02:01"]
the result of optitype A:[A*02:01,A:11:01]
flow cytometry A*02
I have four sample is the A*02 ,but all is not right(for your arcasHLA,but opitype is right)
Which step is wrong?