getSeqFromUCSC: Get DNA sequences from UCSC genome database directly through...

In zeropin/TFCookbook: Analyzing protein-DNA interactions data in principled way

Get DNA sequences from UCSC genome database directly through REST API

Description

Get DNA sequences from UCSC genome database directly through REST API

Usage

getSeqFromUCSC(genome, names, start = NA, end = NA, strand = "+")

Arguments

genome	genome assembly name, hg38, mm10, panPan3, etc
names	either a GRanges object or a character of the chromosome name
start, end	Vector of integers (eventually with NAs) specifying the locations of the subsequences to extract
strand	Vector of integers (eventually with NAs) specifying the locations of the subsequences to extract

Examples

getSeqFromUCSC("hg38", "chr1", start=55, end=65, strand="-")

ranges = GenomicRanges::GRanges(seqnames = "chrM", ranges = IRanges::IRanges(15466, 15555), strand="+")
getSeqFromUCSC("panPan3", names=ranges)

zeropin/TFCookbook documentation built on July 8, 2023, 2:59 p.m.