cbcrg/melanogaster-pergola-reproduce

Name: melanogaster-pergola-reproduce

Owner: Notredame Lab

Description: D. melanogaster dataset Pergola paper analysis

Forked from: JoseEspinosa/melanogaster-pergola-reproduce

Created: 2017-11-28 09:22:03.0

Updated: 2017-11-28 09:22:06.0

Pushed: 2018-01-08 16:55:51.0

Homepage: null

Size: 28552

Language: R

GitHub Committers

User	Most Recent Commit	# Commits

Other Committers

User	Email	Most Recent Commit	# Commits

README

melanogaster-pergola-reproduce.nf

This repository contains the software, scripts and data to reproduce the results corresponding to the D. melanogaster experiment of the Pergola paper.

If you have not install yet docker and nextflow, follow this intructions

Clone the repository

clone --recursive https://github.com/cbcrg/melanogaster-pergola-reproduce.git
elanogaster-pergola-reproduce

Data

Data is publicly available in Zenodo as a compressed tarball .

Data can be downloaded and uncompressed using the following command:

r data
 -O- https://zenodo.org/record/1067836/files/melanogaster_dataset.tar.gz | tar xz -C data

Original Data Sources

The original data can be downloaded from the following source. This data has to be processes using Jaaba to annotated chase behavior from the video recordings available on this link.

Pull docker image

Pull the Docker image use for processing data with Pergola (Pergola and its dependencies installed)

er pull pergola/pergola@sha256:0737f3e70dde73d0272a0be37e05a36a6fed390c8820c5d2834076b711ab707f

Run nextflow pipeline

Once data is downloaded, it is possible to reproduce all the results using this command:

VER=0.26.4 nextflow run melanogaster-pergola-reproduce.nf \
--scores='data/scores/scores_chase_*.mat' \
--var_dir='data/perframe_*' \
--variables="velmag" \
--mappings='data/mappings/jaaba2pergola.txt' \
-with-docker

Results

The previous command generates a results folder that contains the plots used in the paper figure:

• A boxplot comparing the fraction of time performing chase behavior of the GAL4 mutant and the control group
  
• Two figures created using Gviz displaying the intervals annotated as chasing behavior from the GAL4 and the pBDPGAL4 groups.
• Two figures created using Sushi displaying the intervals annotated as chasing behavior from the GAL4 and the pBDPGAL4 groups.
• A folder containing all the necessary files to render the intervals annotated as chasing behavior from the GAL4 and the pBDPGAL4 groups using IGV