copy_validate: copy_validate

In copyseparator: Assembling Long Gene Copies from Short Read Data

copy_validate

Description

A tool to help identify incorrectly assembled chimeric sequences.

Usage

copy_validate(filename, copy_number, read_length, verbose = 1)

Arguments

filename	A DNA alignment in fasta format that contains sequences of two or more gene copies (e.g. results from "copy_assemble").
copy_number	An integer (e.g. 2,3, or 4) giving the number of gene copies in the input file.
read_length	An integer (e.g. 250, or 300) giving the read length of your Next-generation Sequencing data.
verbose	Turn on (verbose=1; default) or turn off (verbose=0) the output.

Value

A histogram in pdf format showing the relationships between the physical distance between neighboring variable sites and read length.

Examples

## Not run: 
copy_validate("inst/extdata/Final_two_copies.fasta",2,300,1)

## End(Not run)

copyseparator documentation built on Nov. 25, 2022, 1:06 a.m.