make_reference: Build gene start-end reference from a gtf file

In VCCRI/Sierra: PolyA counting and differential transcript usage analysis for scRNA-seq data

Build gene start-end reference from a gtf file

Description

Build gene start-end reference from a gtf file

Usage

make_reference(
  gtf_file,
  chr.names = NULL,
  filter.chr = FALSE,
  gene.symbol.ref = "gene_name"
)

Arguments

gtf_file	gtf file
chr.names	a list of valid chromosome names to use
filter.chr	whether to filter chromosomes in the GTF file
gene.symbol.ref	field in the GTF file containing the gene symbol Takes a GTF file as input and creates a table of chromosome start-end positions for each gene. Works with GTF files downloaded from 10x Genomics website.

VCCRI/Sierra documentation built on July 3, 2023, 6:39 a.m.