subset_downsize: subset_downsize

In copyseparator: Assembling Long Gene Copies from Short Read Data

subset_downsize

Description

Subdivides the imported read alignment into subsets and then downsizes each subset by deleting those sequences that have too many gaps or missing data.

Usage

subset_downsize(filename, read_length, overlap, 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.
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.
verbose	Turn on (verbose=1; default) or turn off (verbose=0) the output.

Value

A number of overlapping subsets (before and after downsizing) of the input alignment.

Examples

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

## End(Not run)

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