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TRON-Bioinformatics / seq2HLA

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.
MIT License
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Can I use seq2HLA for cancer scRNA-seq data? #5

Open levinhein opened 3 years ago

levinhein commented 3 years ago

Can I use seq2HLA for cancer scRNA-seq data?

sebboegel commented 3 years ago

Dear levinhein,

i havent tried this yet. In principle it works for any paired end fastq as input. However, the lower the expression (i.e. the lower the number of reads), the more insecure are the results. Maybe give it a try with pseudo-bulk as comparison. I would be very interested in the results.

Sebastian seb.boegel@gmail.com