copy_separate {copyseparator}

copy_separate

Description

Separates two or more gene copies from short-read Next-Generation Sequencing data into a small number of overlapping DNA sequences.

Usage

copy_separate(
  filename,
  copy_number,
  read_length,
  overlap = 225,
  rare_read = 10,
  verbose = 1
)

Arguments

filename

A fasta file contains thousands of short reads that have been mapped to a reference. The reference and reads that are not directly mapped to the reference need to be removed after mapping.

copy_number

An integer (e.g. 2,3, or 4) giving the anticipated 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. This method is designed for read length >=250bp.

overlap

An integer describing number of base pairs of overlap between adjacent subsets. More overlap means more subsets. Default 225.

rare_read

A positive integer. During clustering analyses, clusters with less than this number of reads will be ignored. Default 10.

verbose

Turn on (verbose=1; default) or turn off (verbose=0) the output.

Value

A fasta alignment of a small number of overlapping DNA sequences covering the entire length of the target gene. Gene copies can be assembled by reordering the alignment manually or use the function "copy_assemble".

Examples

## Not run: 
copy_separate("inst/extdata/toydata.fasta",2,300,225,10,1)

## End(Not run)