bt.getfasta: Extract DNA sequences from a fasta file based on feature...

In PhanstielLab/bedtoolsr: Bedtools Wrapper

Extract DNA sequences from a fasta file based on feature coordinates.

Description

Extract DNA sequences from a fasta file based on feature coordinates.

Usage

bt.getfasta(
  fi,
  bed,
  fo = NULL,
  name = NULL,
  nameplus = NULL,
  nameOnly = NULL,
  split = NULL,
  tab = NULL,
  bedOut = NULL,
  s = NULL,
  fullHeader = NULL,
  rna = NULL,
  output = NULL
)

Arguments

fi	<fasta>
bed	<bed/gff/vcf>
fo	Output file (opt., default is STDOUT
name	Use the name field and coordinates for the FASTA header
nameplus	(deprecated) Use the name field and coordinates for the FASTA header
nameOnly	Use the name field for the FASTA header
split	Given BED12 fmt., extract and concatenate the sequences from the BED "blocks" (e.g., exons)
tab	Write output in TAB delimited format.
bedOut	Report extract sequences in a tab-delimited BED format instead of in FASTA format. - Default is FASTA format.
s	Force strandedness. If the feature occupies the antisense, strand, the sequence will be reverse complemented. - By default, strand information is ignored.
fullHeader	Use full fasta header. - By default, only the word before the first space or tab is used.
rna	The FASTA is RNA not DNA. Reverse complementation handled accordingly.
output	Output filepath instead of returning output in R.

PhanstielLab/bedtoolsr documentation built on Aug. 29, 2024, 5:37 p.m.