Templated Mutagenesis 1

This repository contains all of the code required to reproduce the figures and tables in the paper Lack of evidence for a substantial rate of templated mutagenesis in B cell diversification by Julia Fukuyama, Branden J Olson, and Frederick A Matsen IV.

How to use it

A Docker image containing partis, PyMotifFinder, their dependencies, and the R packages required to run the analysis scripts is available on Quay, and can be obtained by running the following commands:

docker pull quay.io/matsengrp/templatedmutagenesis1
docker tag quay.io/matsengrp/templatedmutagenesis1 matsengrp/templatedmutagenesis1

That docker image is built automatically from this repository. If you wish can also build it yourself via

docker build -t matsengrp/templatedmutagenesis1 .

Main analysis

The following commands will reproduce the figures in the paper, placing them in an output directory:

wget https://zenodo.org/record/3741809/files/templated-mutagenesis-data-v3.tar.gz
tar xzf templated-mutagenesis-data-v3.tar.gz
mkdir output
docker run --mount src=${PWD}/data,target=/templatedmutagenesis1/data,type=bind,readonly=true \
    --mount src=${PWD}/output,target=/templatedmutagenesis1/output,type=bind \
    -t matsengrp/templatedmutagenesis1 scons

The analysis takes several hours to complete.

Instructions for running the supplementary analysis as well as results can be found here.