1. Jie Huang
  2. rna_motifs

Overview

============
INSTALLATION
============

* clone software repository from Bitbucket:

hg clone https://rogrro@bitbucket.org/rogrro/rna_motifs

* build GeCo++ software:

cd gMotifs
mkdir build
cd build
cmake ../
make

* add root folder to Python path:

export PYTHONPATH=$PYTHONPATH:/path_to_bitbucket_root_folder

* R needs to be installed on your system with 3 additional libraries:

install.packages(“lattice”)
install.packages(“latticeExtra”)
install.packages(“bootstrap”)

============
NOVA EXAMPLE
============

* edit configuration file:

nova.n.config
nova.r.config

and change paths to reflect absolute values for your system.

* download and prepare mouse mm9 genome by running:

cd m3_light
cd genomes
./mm9.download.sh

* change back to root folder and run the analysis:

./run_nova.sh

This will produce results in the config file results folder.

=================================
GeCo++ COMMAND LINE DOCUMENTATION
=================================

* couting

Run ./counting scripts to count the number of exons with tetramer occurrencies in the region of interest r1,r2,r3:

./counting -c configuration_file.txt
	
i.e ./counting  -c config.txt

* tetramers

Run ./tetramer to calculate the positional specific tetramer occurrences along the RNA splicing map:

./tetramer -c configuration_file.txt
	
=========
R SCRIPTS
=========

* bootstrap analysis

Rscript bootstrap-FDR.R abs_path_working_directory analysis_folder #bootstrap

For example, if your results are in the folder “Nova” under “/Working/directory/” folder (/Working/directory/Nova/), your command will be:

Rscript bootstrap-FDR.R /Working/directory Nova 10000

* tetramer selection

Rscript selection_of_tetramers.R full_path_working_dir  analysis_folder  #bootstrap FDR_cutoff empirical_cutoff

Example:
	
Rscript selection_of_tetramers.R /Working/directory Nova 10000 0.1 0.005

============
FILE FORMATS
============

* configuration file

organism=Mouse/Human
splicing_change_file=/path/to/your/splicing_file.txt
tetramer_folder=/path/to/your/tetreames_folder/
results_folder=/path/to/your/result_folder
search=R/N

The organism flag must be either “Mouse” or “Human” ; the search flag must be either “R” for RSWY analysis or “N” for not redudant tetramer analysis.