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TRON-Bioinformatics / splice2neo

R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes
https://tron-bioinformatics.github.io/splice2neo
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hg38 reference genome #2

Open Elisa89m opened 4 months ago

Elisa89m commented 4 months ago

Hi, Is it possible to run splice2neo by using hg38 genome reference sequence?

Thank you in advance.

Elisa

ibn-salem commented 3 months ago

Thanks for the question. Yes, this is possible.

Just use the respective reference annoations. E.g.

libraray("BSgenome.Hsapiens.UCSC.hg38")
bsg <- BSgenome.Hsapiens.UCSC.hg38

and

# use gtf file of choice and transform into transcript database
gtf_file <- "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_46/gencode.v46.annotation.gtf.gz"

# parse GTF file as txdb object
txdb <- GenomicFeatures::makeTxDbFromGFF(gtf_file)