CD2H gitForager

cbcrg/celegans-pergola-reproduce

Name: celegans-pergola-reproduce

Owner: Notredame Lab

Description: C. elegans dataset Pergola paper analysis

Forked from: JoseEspinosa/celegans-pergola-reproduce

Created: 2017-11-28 09:21:57.0

Updated: 2017-11-28 09:22:01.0

Pushed: 2018-01-08 16:59:08.0

Homepage: null

Size: 199739

Language: R

GitHub Committers

User	Most Recent Commit	# Commits

Other Committers

User	Email	Most Recent Commit	# Commits

README

celegans-pergola-reproduce.nf

CircleCI status

This repository contains the software, scripts and data to reproduce the results corresponding to the C.elegans data of the Pergola paper.

Clone the repository

clone --recursive https://github.com/cbcrg/celegans-pergola-reproduce.git
elegans-pergola-reproduce

Data

The data used for the paper analysis has been gathered and is publicly available at Zenodo as a compressed tarball .

Data can be downloaded and uncompressed using the following command:

r data
 -O- https://zenodo.org/record/1101067/files/celegans_dataset.tar.gz | tar xz -C data

Note: If you prefer to download the data from the original data sources go to original data sources section

Pull docker image

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

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 paper results using this command:

VER=0.26.4 nextflow run celegans-pergola-reproduce.nf \
--strain1_trackings 'data/unc_16/*.hdf5' \
--strain2_trackings 'data/N2/*.hdf5' \
--mappings_speed 'data/mappings/worms_speed2p.txt' \
--mappings_bed 'data/mappings/bed2pergola.txt' \
--mappings_motion data/mappings/worms_motion2p.txt \
-with-docker

Results

The nextflow pipeline produces a results folder containing:

Three plots comparing the distribution of unc-16 and N2 mid body speed when moving forward, backward and when paused, respectively.
A figure created using Gviz depicting in a heatmap the mid body speed of unc-16 and N2 C.elegans strains.
A figure created using Sushi rendering in a heatmap the mid body speed of unc-16 and N2 C.elegans strains.
A folder containing all the necessary files to compare mid body speed of the two strains in a heatmap using IGV. Data is separated in folders corresponding to each mouse group. See below for a detailed explanation of how to load the data on IGV.

IGV visualization

You can use the version we adapted of the Integrative Genomics Viewer (or the original one) to browse the resulting data (as we did for the paper). However IGV does not allow extended programatic access to set the graphical options, hence our script produces a heatmap reproducing the paper figure. This file can be found inside the heatmap results folder.

Adapted IGV version

We adapted IGV to display temporal data incorporating minor changes. To do so we fork the IGV git repository into but we call IBB (Integrative Behavioral Browser)

You can clone and build IBB using the following commands:

Note: If you prefer to use the original IGV you can download from here

clone --recursive https://github.com/JoseEspinosa/IBB.git

BB/
-f build.xml
b.sh

Go to the menu Genomes –> Create .genome File .. Select the fasta file created in the results/igv folder and click on OK and save the genome in your system as shown in the snapshot below:

snapshot create-genome

Open the tracks in .bedGraph format from the /results/igv/results_bedgr1_igv folder from the menu File –> Load from File…

Select all the tracks clicking on their name and right click to display options, and select the options as in the snaphot below:

snapshot create-genome

Do the same with the data of the N2 strain placed inside /results/igv/results_bedgr2_igv.

Finally click on the same menu the Set Heatmap Scale option and select the configure it as in the image:

snapshot create-genome

Original Data Sources

~~If you prefer, you can download the data from the original sources~~: ~~N2 C.elegans strain (control) behavioral recordings: N2~~ ~~unc-16 C.elegans strain behavioral recordings: unc-16~~

The database has been migrated and the data can now be accessed at this link

Actually, the DB points to records hosted in Zenodo as well. If you prefer to download the data from original Zenodo records used the following links:

unc-16 data

s://zenodo.org/record/1031398/files/unc-16 (e109) on food R_2009_12_09__11_53_42___2___5_features.hdf5 
s://zenodo.org/record/1030731/files/unc-16 (e109) on food L_2009_12_09__11_52_59___1___5_features.hdf5 
s://zenodo.org/record/1030675/files/unc-16 (e109) on food L_2009_12_09__11_56_23___8___6_features.hdf5 
s://zenodo.org/record/1030635/files/unc-16 (e109) on food R_2009_12_11__12_21_06___1___2_features.hdf5 
s://zenodo.org/record/1030551/files/unc-16 (e109) on food R_2009_12_10__11_43_22___8___5_features.hdf5 
s://zenodo.org/record/1030449/files/unc-16 (e109) on food L_2009_12_11__12_21___3___2_features.hdf5 
s://zenodo.org/record/1029258/files/unc-16 (e109) on food L_2009_12_11__12_23_44__2_features.hdf5 
s://zenodo.org/record/1029107/files/unc-16 (e109) on food R_2009_12_10__11_42___3___5_features.hdf5 
s://zenodo.org/record/1028861/files/unc-16 (e109) on food L_2009_12_10__11_42_17___2___5_features.hdf5 
s://zenodo.org/record/1028581/files/unc-16 (e109) on food L_2009_12_09__11_56_41___7___5_features.hdf5 
s://zenodo.org/record/1028255/files/unc-16 (e109) on food R_2009_12_11__12_21_48___2___2_features.hdf5 
s://zenodo.org/record/1027743/files/unc-16 (e109) on food R_2009_12_09__11_53___3___5_features.hdf5 
s://zenodo.org/record/1026603/files/unc-16 (e109) on food L_2009_12_11__12_23_10___7___2_features.hdf5 
s://zenodo.org/record/1025348/files/unc-16 (e109) on food L_2009_12_10__11_42_48___4___5_features.hdf5 
s://zenodo.org/record/1023916/files/unc-16 (e109) on food L_2009_12_10__11_43_41___7___5_features.hdf5 
s://zenodo.org/record/1020092/files/unc-16 (e109) on food R_2009_12_10__11_44_17__5_features.hdf5 
s://zenodo.org/record/1007843/files/unc-16 (e109) on food L_2009_12_09__11_54_10___4___5_features.hdf5 
s://zenodo.org/record/1003973/files/unc-16 (e109) on food R_2009_12_11__12_21_49___6___2_features.hdf5 
s://zenodo.org/record/1003866/files/unc-16 (e109) on food R_2009_12_10__11_42_21___6___5_features.hdf5 
s://zenodo.org/record/1003814/files/unc-16 (e109) on food R_2009_12_09__11_55_21___6___5_features.hdf5

N2 data

Note: Only a subset of the N2 files available on the database, those recorded within a 2-week window centered around the unc-16 mutant strain, have been used for the analysis. The detailed list of files is:

s://zenodo.org/record/1033831/files/N2 on food L_2009_12_09__10_31_54___4___1_features.hdf5
s://zenodo.org/record/1030359/files/N2 on food L_2009_12_15__10_22___3___1_features.hdf5
s://zenodo.org/record/1030186/files/N2 on food R_2009_12_09__10_30_41___1___1_features.hdf5
s://zenodo.org/record/1030064/files/N2 on food R_2009_12_10__10_20_42___2___1_features.hdf5
s://zenodo.org/record/1029910/files/N2 on food R_2009_12_09__10_31___3___1_features.hdf5
s://zenodo.org/record/1029792/files/N2 on food R_2009_12_11__12_01_52___2___1_features.hdf5
s://zenodo.org/record/1029719/files/N2 on food R_2009_12_11__12_01_09___1___1_features.hdf5
s://zenodo.org/record/1029463/files/N2 on food L_2009_12_15__10_22_57___2___1_features.hdf5
s://zenodo.org/record/1029166/files/N2 on food R_2009_12_09__10_31_25___2___1_features.hdf5
s://zenodo.org/record/1029005/files/N2 on food R_2009_12_10__10_21_43___8___1_features.hdf5
s://zenodo.org/record/1028853/files/N2 on food R_2009_12_09__10_32_28___8___1_features.hdf5
s://zenodo.org/record/1028265/files/N2 on food L_2009_12_14__10_21___3___1_features.hdf5
s://zenodo.org/record/1028104/files/N2 on food R_2009_12_11__12_04_07___7___1_features.hdf5
s://zenodo.org/record/1027697/files/N2 on food R_2009_12_11__12_01___3___1_features.hdf5
s://zenodo.org/record/1026362/files/N2 on food L_2009_12_15__10_23_42___8___1_features.hdf5
s://zenodo.org/record/1026260/files/N2 on food R_2009_12_15__10_21_50___1___1_features.hdf5
s://zenodo.org/record/1025470/files/N2 on food R_2009_12_14__10_21_06___2___2_features.hdf5
s://zenodo.org/record/1024484/files/N2 on food R_2009_12_15__10_23_59___7___1_features.hdf5
s://zenodo.org/record/1024246/files/N2 on food L_2009_12_14__10_22_12___8___1_features.hdf5
s://zenodo.org/record/1023706/files/N2 on food L_2009_12_11__12_03_49___8___1_features.hdf5
s://zenodo.org/record/1023613/files/N2 on food R_2009_12_14__10_20_23___1___2_features.hdf5
s://zenodo.org/record/1022692/files/N2 on food L_2009_12_10__10_20_00___1___1_features.hdf5
s://zenodo.org/record/1021677/files/N2 on food L_2009_12_10__10_20___3___1_features.hdf5
s://zenodo.org/record/1019655/files/N2 on food L_2009_12_15__10_24_35__1_features.hdf5
s://zenodo.org/record/1017883/files/N2 on food R_2009_12_14__10_23_04__1_features.hdf5
s://zenodo.org/record/1017594/files/N2 on food L_2009_12_14__10_22_30___7___1_features.hdf5
s://zenodo.org/record/1016159/files/N2 on food L_2009_12_10__10_22_01___7___1_features.hdf5
s://zenodo.org/record/1014751/files/N2 on food_2009_12_09__10_33_20__1_features.hdf5 
s://zenodo.org/record/1014381/files/N2 on food_2009_12_09__10_32_45___7___1_features.hdf5 
s://zenodo.org/record/1011907/files/N2 on food L_2009_12_11__12_04_46__1_features.hdf5
s://zenodo.org/record/1008303/files/N2 on food R_2009_12_14__10_21_38___4___1_features.hdf5
s://zenodo.org/record/1007895/files/N2 on food L_2009_12_10__10_21_10___4___1_features.hdf5
s://zenodo.org/record/1004855/files/N2 on food R_2009_12_15__10_22_39___6___1_features.hdf5
s://zenodo.org/record/1003856/files/N2 on food L_2009_12_10__10_20_40___6___1_features.hdf5
s://zenodo.org/record/1003800/files/N2 on food L_2009_12_09__10_31_26___6___1_features.hdf5
s://zenodo.org/record/1017607/files/N2 on food L_2009_12_17__11_05_22___7___2_features.hdf5
s://zenodo.org/record/1024180/files/N2 on food R_2009_12_17__11_04_16___8___1_features.hdf5
s://zenodo.org/record/1027779/files/N2 on food L_2009_12_17__11_02_29___1___1_features.hdf5
s://zenodo.org/record/1008576/files/N2 on food L_2009_12_17__11_03_42___4___1_features.hdf5
s://zenodo.org/record/1005033/files/N2 on food L_2009_12_17__11_03_15___6___1_features.hdf5

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.