Gene Location File - One Gene One Genomic Interval

Question

[jon.klonowski]

I am trying to make a gene location file: Gene_Name Chromosome Start End

So that I can run a program that maps SNPs to genes for burden analysis. My problem is that UCSC table output gives transcripts, and multiple transcripts can be attributed to a single gene. How do I consolidate things so I can end up with a "one gene one genomic interval" model.

bests,

JFK

Answer 1

[wulj2]

interesting problem to solve, but i think it will be easy

Answer 2

[jon.klonowski]

My lab mate sent me some R script:

library(GenomicFeatures)
GENCODE_FILE.GR38 = "/data/projects/annotation/GENCODE/rel29/gencode.v29.annotation.gff3.gz"
#------------ 
# GET TSS FOR PROTEIN CODING GENES
# filter for protein coding transcripts
db = makeTxDbFromGFF(GENCODE_FILE.GR38, format=c("gff3"))
transcripts = transcripts(db, columns=c("tx_id", "tx_name"))
genes = genes(db, columns=c(“tx_id”, “tx_name”))

Where I got the most recent gencode release: https://www.gencodegenes.org/human/