riboraptor : a pipeline for analysing ribosome profiling data

Python package to analyse ribosome profiling data. Most of the functionality has been ported to ribotricer

• Free software: BSD license
• Documentation: https://riboraptor.readthedocs.io/en/latest/

Installation

Setting up conda

1. Install conda, the best way to install it is with the Miniconda package.The Python 3 version is recommended.
2. Set up channels, It is important to add them in this order.

conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

Installing dependencies

We will create a searate environment inside conda for running riboraptor. The environment name is also riboraptor. If you already have a conda environment named riboraptor, you can delete it by running:

source deactivate riboraptor && conda env remove -n riboraptor

We will now install all the dependencies:

conda create --name riboraptor python=3 gcc matplotlib numpy pandas pybedtools \
pyBigWig pyfaidx pysam scipy seaborn statsmodels six click click-help-colors htseq biopython bx-python \
h5py joblib trackhub pytest snakemake sra-tools star fastqc trim-galore ucsc-bedgraphtobigwig ucsc-bedsort \
ucsc-bigwigmerge bamtools pysradb && source activate riboraptor

We also have the following two dependencies for processing and downloading SRA datasets:

1. aspera connect : For allowing '.fasp' downloads from SRA

Linux download link: https://download.asperasoft.com/download/sw/connect/3.7.4/aspera-connect-3.7.4.147727-linux-64.tar.gz

1. SRAdb : For fetching all experiments of a SRA project with the associated metadata

Since there is currently a bug in bioconductor-sradb, we will install it from github.

git clone https://github.com/seandavi/SRAdb
cd SRAdb

Run R, and install SRAdb within R use devtools. Please make sure your riboraptor environment is already activated. (source activate riboraptor):

library(devtools)
devtools::install(".")

And finally, we need two metadata files for processing SRA records:

mkdir riboraptor-data && cd riboraptor-data
wget -c http://starbuck1.s3.amazonaws.com/sradb/GEOmetadb.sqlite.gz && gunzip GEOmetadb.sqlite.gz
wget -c https://starbuck1.s3.amazonaws.com/sradb/SRAmetadb.sqlite.gz && gunzip SRAmetadb.sqlite.gz

Installing riboraptor

source activate riboraptor
git clone https://github.com/saketkc/riboraptor.git
cd riboraptor
python setup.py install --single-version-externally-managed --record=record.txt

We will assume you have the following directory structure for the rest of our analysis:

| some_root_directory
| ├── riboraptor
| │   ├── snakemake
| │   └── setup.py
| ├── riboraptor-data
| │   ├── GEOmetadb.sqlite
| │   └── SRAmetadb.sqlite

Using riboraptor

Usage mode 1: use riboraptor as a Snakemake based workflow

See example workflow

Usage mode 2: use riboraptor as a standalone toolkit

See: https://riboraptor.readthedocs.io/en/latest/

Usage mode 3: ribopod - database

In progress: http://ribopod.usc.edu/

Features

See: https://riboraptor.readthedocs.io/en/latest/cmd-manual.html