/iLoci_Lai2020

Procedures and data for the iLoci study described in Lai et al. (2020)

Primary LanguageJupyter NotebookGNU General Public License v3.0GPL-3.0

iLoci_Lai2020

Procedures and data for the iLoci study described in Lai, Standage and Brendel (2020)

Overview

This repository documents application of AEGeAn code to derive, classify, and analyze genomic interval loci (iLoci) as described in the paper Lai, Standage, and Brendel (2020). Please refer to the AEGeAn Installation site for details on how to obtain the relevant software. The simplest way to get going is to use the AEGeAn Singularity container, e.g. as follows:

cd
git clone https://github.com/BrendelGroup/iLoci_Lai2020
cd iLoci_Lai2020/work
singularity pull --name aegean.simg shub://BrendelGroup/AEGeAn
rws="singularity exec -e -B ~/iLoci_Lai2020 ~/iLoci_Lai2020/work/aegean.simg"
$rws fidibus -h

In the above example, you clone this repository into your Linux home directory, go into the iLoci_Lai2020/work directory that has been created, download the AEGeAn Singularity container, define the shell variable rws ("run with singularity"), and check that everything works by showing the "help" lines for the AEGeAn command fididbus.

To reproduce the data discussed in Lai, Standage and Brendel (2020), go to ./work and follow the instructions in the README file.