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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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Yara DNA vs RNA DBs #12

Closed pintoa1-mskcc closed 2 years ago

pintoa1-mskcc commented 2 years ago

``Hi!

I am trying to utlize your pipeline with hg19 instead of GRCh38. Because of this I am trying to recreate the yara references, but I have never used this tool before so I do not know what exactly to do. Mainly, my concern is the difference between the RNA and DNA references for yara? I had assumed I could simply run

yara_indexer $RefFasta

but this would only give me one database, i'd assume for DNA not RNA. Why are there two databases needed and how can I make them for hg19?

riederd commented 2 years ago

Hello,

thanks for your interest in nextNEOpi.

You do not need to recreate the yara index. It is only used for HLA typing with optitype. Optitype comes with its own reference sequence specific for the HLA genes (see https://github.com/FRED-2/OptiType/tree/master/data)