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hg38 reference genome #2

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Elisa89m opened this issue May 31, 2024 · 1 comment
Open

hg38 reference genome #2

Elisa89m opened this issue May 31, 2024 · 1 comment

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@Elisa89m
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Hi,
Is it possible to run splice2neo by using hg38 genome reference sequence?

Thank you in advance.

Elisa
@ibn-salem
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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)

ibn-salem added a commit that referenced this issue Jun 6, 2024
@ibn-salem
Merge branch 'splice2neo_neoants_incomming' into 'dev'
bc9c495 
Integrate splice2neo_neoants

Closes #1, #2, #10, #17, #13, splice2neo_neoants#21, and #119

See merge request tron/bnt_neoants/splice2neo!119
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@ibn-salem @Elisa89m