extract_promotor_seqs_from_genome: Retrieve all upstream promotor sequences from a genome

In HajkD/metablastr: Perform Massive Local BLAST Searches

Retrieve all upstream promotor sequences from a genome

Description

Given a genome assembly file and an corresponding annotation file users can retrieve all upstream promotor sequences of all genes from a genome.

Usage

extract_promotor_seqs_from_genome(
  annotation_file,
  genome_file,
  promotor_length = 500,
  annotation_format = "gtf",
  file_name = NULL,
  path = NULL,
  update = TRUE
)

Arguments

annotation_file	file path to the annotation file of the genome assembly in gtf or gff format.
genome_file	file path to the genome assembly file.
promotor_length	width of upstream promotors. This is -promotor_width bp from the transcription start site (TSS) of the gene.
annotation_format	format of the annotation file. Options are: annotation_format = "gtf" annotation_format = "gff"
file_name	file path to the output file storing the promotor sequences.
path	a file path to an output folder storing the promotor sequences.
update	shall previously generated promotor sequences be overwritten when again generated for the same genome assembly?

Author(s)

Hajk-Georg Drost

HajkD/metablastr documentation built on Sept. 14, 2023, 5:26 p.m.