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tecontent's Introduction

TEContent

Purpose

Calculates the absolute and relative TE content of a genome.

Requirements

Written in R.

Requires the following R packages:

argparse

Biostrings

Usage

Basic usage is:

TEContent.R --species=species1,species2,species3 --genomefile=genome1.fas,genome2.fas,genome3.fas --tefile=TE1.fas,TE2.fas,TE3.fas --phenotype="Present","Present","Absent"

TEContent takes four mandatory arguments:

--species (comma-separated list of species names)

--genomefile (comma-separated list of genome fasta files)

--tefile (comma-separated list of TE fasta files)

--phenotype (comma-separated list of phenotypes corresponding to each species)

TEContent also accepts three optional flags:

--logx (use log10 scale for x axis)

--logy (use log10 scale for y axis)

--boxplot (generate boxplot output as well as scatterplot)

tecontent's People

Contributors

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Stargazers

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Watchers

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