index_fa: Indexes the FASTA file, and generates a 'chrom.sizes' file

In HarteminkLab/TOP: Predict transcription factor occupancy using DNase- or ATAC-seq data

Indexes the FASTA file, and generates a ‘chrom.sizes’ file

Description

Indexes the FASTA file, and generates a ‘chrom.sizes’ file with chromosome numbers and the size of each chromosome.

Usage

index_fa(fa_file, chromsize_file = "chrom.sizes", outdir = dirname(fa_file))

Arguments

fa_file	FASTA file of reference genome sequence.
chromsize_file	Path of the output ‘chrom.sizes’ file.
outdir	Output directory (default: saves to the directory of the FASTA file).

Examples

## Not run: 
index_fa('hg38.fa', chromsize_file='hg38.chrom.sizes')

## End(Not run)

HarteminkLab/TOP documentation built on July 27, 2023, 6:14 p.m.