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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Can I use the bowtie index file in the subdirectory 'reference' #13
Thanks for creating the package!
I'm a bit confused on the bowtie index files required, do I have to do the index file using bowtie by myself or I can directly use the 'reference' folder in the subdirectory under seq2HLA?
Hi Sebastian,
Thanks for creating the package! I'm a bit confused on the bowtie index files required, do I have to do the index file using bowtie by myself or I can directly use the 'reference' folder in the subdirectory under seq2HLA?
I look forward to your reply.
Best, Jing