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.
Hello,
I am trying to apply seq2HLA to my RNA-seq data (paired-end). When I run it, I get the following result.
reads processed: 18902737
reads with at least one reported alignment: 40 (0.00%)
reads that failed to align: 18902697 (100.00%)
Reported 3460 paired-end alignments to 1 output stream(s)
For the rest of the samples something very similar happens. I have used bowtie2 with those samples to align and have not encountered any problems. Can you give me a solution?
Hello, I am trying to apply seq2HLA to my RNA-seq data (paired-end). When I run it, I get the following result.
reads processed: 18902737
reads with at least one reported alignment: 40 (0.00%)
reads that failed to align: 18902697 (100.00%)
Reported 3460 paired-end alignments to 1 output stream(s) For the rest of the samples something very similar happens. I have used bowtie2 with those samples to align and have not encountered any problems. Can you give me a solution?
Thank you very much for your help.