find_FASTA: find_FASTA

In c1au6i0/crispR: find protospacers

Description

Function to identify all candidate guide (protospacer) sequences in a FASTA file. Note that the genomic coordinates are 1-indexed and fully closed.

Usage

find_FASTA(
  file_fasta,
  chr = 7,
  start = 117465784,
  end = 117466784,
  l = 20,
  PAM = "NGG"
)

Arguments

file_fasta	path to a file FASTA (either compressed or not).
chr	chromosome.
start	start of the DNA sequence to scan for protospacers.
end	end of the DNA sequence to scan for protospacers.
l	protospacer length.
PAM	PAM sequence to match.

Value

a dataframe with columns:

1. chr.

2. start.

3. end.

4. protospacer sequence.

5. PAM sequence (e.g. CGG as the sequence that matched the PAM sequence NGG).

6. Strand (+ or -).

c1au6i0/crispR documentation built on Feb. 27, 2020, 12:42 a.m.