restrictionDigest: Simulate DNA fragmentation with restriction enzymes.

In fischuu/GenomicTools: Collection of Tools for Genomic Data Analysis

Simulate DNA fragmentation with restriction enzymes.

Description

This function determines the expected fragments from a DNA fragmentation with restriction enzymes.

Usage

  restrictionDigest(fa, re1="AATTC", re2="GCATG", use.rev=TRUE)

Arguments

fa	A reference genome in fasta format
re1	The first restriction enzyme sequence
re2	The second restriction enzyme sequence
use.rev	Logical, should the reverse complement be used

Details

This is a very early quick+dirty tool to perform that step and it needs more functions and performance improvements as well as input check. Further, it currently only works with two restriction enzymes.

Value

A list containing the clusters (clusters) and their lengths (codecluster.bp)

Author(s)

Daniel Fischer

fischuu/GenomicTools documentation built on April 30, 2023, 7:53 p.m.