subset_downsize

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

Assembles two or more gene copies from short-read Next-Generation Sequencing data. Works best when there are only two gene copies and read length >=250 base pairs. High and relatively even coverage are important.

Lei Yang

copyseparator

Assembling Long Gene Copies from Short Read Data

subset_downsize function

<dl><dt>filename</dt>
<dd>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.</dd>
<dt>read_length</dt>
<dd>An integer (e.g. 250, or 300) giving the read length of your Next-generation Sequencing data. This method is designed for read length &gt;=250bp.</dd>
<dt>overlap</dt>
<dd>An integer describing number of base pairs of overlap between adjacent subsets. More overlap means more subsets.</dd>
<dt>verbose</dt>
<dd>Turn on (verbose=1; default) or turn off (verbose=0) the output.</dd></dl>

Arguments

subset_downsize — subset_downsize

<dl>

<dt>filename</dt>
<dd>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.</dd>


<dt>read_length</dt>
<dd>An integer (e.g. 250, or 300) giving the read length of your Next-generation Sequencing data. This method is designed for read length &gt;=250bp.</dd>


<dt>overlap</dt>
<dd>An integer describing number of base pairs of overlap between adjacent subsets. More overlap means more subsets.</dd>


<dt>verbose</dt>
<dd>Turn on (verbose=1; default) or turn off (verbose=0) the output.</dd>

</dl>

subset_downsize: subset_downsize

Description

Usage

Value

Arguments

Examples