In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.
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allele 1 is missing in the run2-ClassI-class.HLAgenotype4digits #16
A no NA A24:02 0.165067
B no NA B54:01 0.03863101
C no NA no NA
where did i RUN it wrong?
python /home/ranzhi/seq2HLA-master-C12/seq2HLA-master/seq2HLA.py -1 /home/ranzhi/seq2HLA-master-C12/C12/C12CA-Req9_FKDL210264010-1a_1.fastq -2 /home/ranzhi/seq2HLA-master-C12/C12/C12CA-Req9_FKDL210264010-1a_2.fastq -r /home/ranzhi/seq2HLA-master-C12/run1 -p 10
this is my code
Locus Allele 1 Confidence Allele 2 Confidence
A no NA A24:02 0.165067 B no NA B54:01 0.03863101 C no NA no NA where did i RUN it wrong? python /home/ranzhi/seq2HLA-master-C12/seq2HLA-master/seq2HLA.py -1 /home/ranzhi/seq2HLA-master-C12/C12/C12CA-Req9_FKDL210264010-1a_1.fastq -2 /home/ranzhi/seq2HLA-master-C12/C12/C12CA-Req9_FKDL210264010-1a_2.fastq -r /home/ranzhi/seq2HLA-master-C12/run1 -p 10 this is my code