omniclip 0.2.1

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omniCLIP

omniCLIP is a Bayesian peak caller that can be applied to data from CLIP-Seq experiments to detect regulatory elements in RNAs.

Overview

Introduction

Dependencies

Installation

Usage

Contributors

License

Introduction

omniCLIP can call peaks for CLIP-Seq data data while accounting for confounding factors such as the gene expression and it automatically learns relevant diagnostic events from the data. Furtermore, it can leverage replicate information and model technical and biological variance.

Dependencies and Requirements

omniCLIP requires Python (v.3.7) and the libraries described in the environment.yml file. All required dependencies can be installed using conda by executing the following in the main project directory :

$ conda env create -f environment.yml

The environment then needs to be activated in order to run omniCLIP :

$ conda activate omniEnv

Installation

Manual installation

The latest stable release in the master branch can be downloaded by executing:

$ git clone -b master https://github.com/simojoe/omniCLIP.git

After this the following command has to be executed:

$ python3 setup.py

This compiles the Cython code for the viterbi algorithm.

Usage

An omniCLIP analysis is run into four different steps :

• Generating the annotation database
• Parsing the background RNA-seq files
• Parsing the CLIP files
• Running the omniCLIP algorithm

The following is an example of the commands. The commands in this example only show the required arguments for the analysis. The following files are necessary to run an analysis.

File name	Description
$GFF_file	Genome annotation file
$GENOME_dir	Directory containing FASTA files with each of the chromosomes sequence
$BG_file[1,2,...]	BAM files for the background library. The alignments need to have the MD and NM tags.
$CLIP_file[1,2,...]	BAM files for the CLIP library. The alignments need to have the MD and NM tags.

The following files will be created.

File name	Description
$DB_file	SQL database of the genome annotation.
$BG_dat	H5PY file of the parsed background library.
$CLIP_dat	H5PY file of the parsed CLIP library.
$OUT_dir	Directory containing the final results

1. Generating the annotation database

$ python3 omniCLIP.py generateDB \
--gff-file $GFF_file --db-file $DB_file

2. Parsing the background RNA-seq files

$ python3 omniCLIP.py parsingBG \
--db-file $DB_file --genome-dir $GENOME_dir \
--bg-files $BG_file1 --bg-files $BG_file2 \
--out-file $BG_dat

3. Parsing the CLIP files

$ python3 omniCLIP.py parsingCLIP \
--db-file $DB_file --genome-dir $GENOME_dir \
--clip-files $CLIP_file1 --clip-files $CLIP_file2 \
--out-file $CLIP_dat

4. Running the omniCLIP algorithm

$ python3 omniCLIP.py run_omniCLIP \
--db-file $DB_file --bg-dat $BG_dat --clip-dat $CLIP_dat \
--out-dir $OUT_dir

Optional arguments

For the full list of optional arguments of the different step, consult the help of the commands using :

$ python3 omniCLIP.py parsingBG --help

Contributors

License

GNU GPL license (v3)