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https://github.com/YeoLab/outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
https://github.com/YeoLab/outrigger

Last synced: 7 days ago
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Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data

Host: GitHub
URL: https://github.com/YeoLab/outrigger
Owner: YeoLab
License: bsd-3-clause
Created: 2015-11-23T21:37:31.000Z (over 8 years ago)
Default Branch: master
Last Pushed: 2020-04-10T22:48:49.000Z (about 4 years ago)
Last Synced: 2024-05-07T05:21:44.655Z (about 2 months ago)
Language: Python
Homepage: http://yeolab.github.io/outrigger/
Size: 183 MB
Stars: 60
Watchers: 35
Forks: 22
Open Issues: 46
Metadata Files:
- Readme: README.rst
- Changelog: HISTORY.rst
- Contributing: CONTRIBUTING.rst
- License: LICENSE

Lists

awesome-alternative-splicing - outrigger - calculate alternative splicing scores of RNA-Seq data based on junction reads and a de novo, custom annotation created with a graph database, especially made for single-cell analyses. (Software)
awesome_single_cell - outrigger - [Python] - Outrigger is a program to calculate alternative splicing scores of RNA-Seq data based on junction reads and a *de novo*, custom annotation created with a graph database, especially made for single-cell analyses. (Software packages / RNA-seq)
awesome-single-cell - outrigger - [Python] - Outrigger is a program to calculate alternative splicing scores of RNA-Seq data based on junction reads and a *de novo*, custom annotation created with a graph database, especially made for single-cell analyses. (Software packages / RNA-seq)
awesome-single-cell - outrigger - [Python] - Outrigger is a program to calculate alternative splicing scores of RNA-Seq data based on junction reads and a *de novo*, custom annotation created with a graph database, especially made for single-cell analyses. (Software packages / RNA-seq)

README

.. -*- mode: rst -*-

|OutriggerLogo|

|BuildStatus|\ |codecov|\ |PyPIVersions|\ |PythonVersionCompatibility|

.. |OutriggerLogo| image:: https://raw.githubusercontent.com/YeoLab/outrigger/master/logo/logo-1x.png
:target: https://github.com/YeoLab/outrigger
.. |BuildStatus| image:: https://travis-ci.org/YeoLab/outrigger.svg?branch=master
:target: https://travis-ci.org/YeoLab/outrigger
.. |codecov| image:: https://codecov.io/gh/YeoLab/outrigger/branch/master/graph/badge.svg
:target: https://codecov.io/gh/YeoLab/outrigger
.. |PyPIVersions| image:: https://img.shields.io/pypi/v/outrigger.svg
:target: https://pypi.python.org/pypi/outrigger
.. |PythonVersionCompatibility| image:: https://img.shields.io/pypi/pyversions/outrigger.svg
:target: https://pypi.python.org/pypi/outrigger

=============================================================================
Large-scale detection and calculation of alternative splicing with Outrigger_
=============================================================================

Outrigger_ is a program which uses junction reads from RNA seq data, and
a graph database to create a *de novo* alternative splicing annotation
with a graph database, and quantify percent spliced-in (Psi) of the
events.

- Free software: BSD license
- Documentation is available here: http://yeolab.github.io/outrigger/

Features
========

- Finds novel splicing events, including novel exons!
(``outrigger index``) from ``.bam`` files
- (optional) Validates that exons have correct splice sites, e.g. GT/AG
and AT/AC for mammalian systems (``outrigger validate``)
- Calculate "percent spliced-in" (Psi/Ψ) scores for all your samples
given the validated events (or the original events if you opted not
to validate) via ``outrigger psi``

|OutriggerOverview|

.. |OutriggerOverview| image:: https://raw.githubusercontent.com/YeoLab/outrigger/master/docs/_static/outrigger_overview-300ppi.png
:target: https://raw.githubusercontent.com/YeoLab/outrigger/master/docs/_static/outrigger_overview-300ppi.png

Installation
============

To install ``outrigger``, we recommend using the `Anaconda Python
Distribution `__ and creating an environment.

You'll want to add the `bioconda `__
channel to make installing `bedtools `__ and
its Python wrapper, `pybedtools `__
easy (these programs are necessary for both ``outrigger index`` and
``outrigger validate``).

conda config --add channels r
conda config --add channels bioconda

Create an environment called ``outrigger-env``. Python 2.7, Python 3.4, Python 3.5, and Python 3.6 are supported.

conda create --name outrigger-env outrigger

Now activate that environment:

source activate outrigger-env

To check that it installed properly, try the command with the help
option (``-h``), ``outrigger -h``. The output should look like this:

$ outrigger -h
usage: outrigger [-h] [--version] {index,validate,psi} ...

outrigger (1.0.0dev). Calculate "percent-spliced in" (Psi) scores of
alternative splicing on a *de novo*, custom-built splicing index -- just for
you!

positional arguments:
{index,validate,psi} Sub-commands
index Build an index of splicing events using a graph
database on your junction reads and an annotation
validate Ensure that the splicing events found all have the
correct splice sites
psi Calculate "percent spliced-in" (Psi) values using the
splicing event index built with "outrigger index"

optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit

Bleeding edge code from Github (here)
-------------------------------------

For advanced users, if you have `git `__ and
`Anaconda Python `__ installed, you
can:

#. Clone this repository
#. Change into that directory
#. Create an environment named ``outrigger-env`` with the necessary packages
from Anaconda and the Python Package Index (PyPI).
#. Activate the environment

These steps are shown in code below.

git clone https://github.com/YeoLab/outrigger.git
cd outrigger
conda env create --file environment.yml
source activate outrigger-env

Quick start
===========

If you just want to know how to run this on your data with the default
parameters, start here. Let's say you performed your alignment in the
folder called ``~/projects/tasic2016/analysis/tasic2016_v1``, and that's
where your ``SJ.out.tab`` files from the STAR aligner are (they're
output into the same folder as the ``.bam`` files). First you'll need to
change directories to that folder with ``cd``.

cd ~/projects/tasic2016/analysis/tasic2016_v1

Then you need find all alternative splicing events, which you do by
running ``outrigger index`` on the splice junction files and the gtf.
Here is an example command:

Input: ``.SJ.out.tab`` files
----------------------------

outrigger index --sj-out-tab *SJ.out.tab \
--gtf /projects/ps-yeolab/genomes/mm10/gencode/m10/gencode.vM10.annotation.gtf

Input: ``.bam`` files
---------------------

If you're using ``.bam`` files instead of ``SJ.out.tab`` files, never despair!
Below is an example command. Keep in mind that for this program to work, the
events must be sorted and indexed.

outrigger index --bam *sorted.bam \
--gtf /projects/ps-yeolab/genomes/mm10/gencode/m10/gencode.vM10.annotation.gtf

Next, you'll want to validate that the splicing events you found follow
biological rules, such as being containing GT/AG (mammalian major
spliceosome) or AT/AC (mammalian minor splicesome) sequences. To do
that, you'll need to provide the genome name (e.g. ``mm10``) and the
genome sequences. An example command is below:

outrigger validate --genome mm10 \
--fasta /projects/ps-yeolab/genomes/mm10/GRCm38.primary_assembly.genome.fa

Finally, you can calculate percent spliced in (Psi) of your splicing
events! Thankfully this is very easy:

outrigger psi

It should be noted that ALL of these commands should be performed in the
same directory, so no moving.

Quick start summary
-------------------

Here is a summary the commands in the order you would use them for
outrigger!

cd ~/projects/tasic2016/analysis/tasic2016_v1
outrigger index --sj-out-tab *SJ.out.tab \
--gtf /projects/ps-yeolab/genomes/mm10/gencode/m10/gencode.vM10.annotation.gtf
outrigger validate --genome mm10 \
--fasta /projects/ps-yeolab/genomes/mm10/GRCm38.primary_assembly.genome.fa
outrigger psi

This will create a folder called ``outrigger_output``, which at the end
should look like the one below. Each file and folder is annotated with which command
produced it.

$ tree outrigger_output
outrigger_output..........................................................index
├── index.................................................................index
│   ├── gtf...............................................................index
│   │   ├── gencode.vM10.annotation.gtf...................................index
│   │   ├── gencode.vM10.annotation.gtf.db................................index
│   │   └── novel_exons.gtf...............................................index
│   ├── exon_direction_junction_triples.csv...............................index
│   ├── mxe...............................................................index
│   │   ├── event.bed.....................................................index
│   │   ├── events.csv....................................................index
│   │   ├── exon1.bed.....................................................index
│   │   ├── exon2.bed.....................................................index
│   │   ├── exon3.bed.....................................................index
│   │   ├── exon4.bed.....................................................index
│   │   ├── intron.bed....................................................index
│   │   ├── splice_sites.csv...........................................validate
│   │   └── validated..................................................validate
│   │   └── events.csv.............................................validate
│   └── se................................................................index
│   ├── event.bed.....................................................index
│   ├── events.csv....................................................index
│   ├── exon1.bed.....................................................index
│   ├── exon2.bed.....................................................index
│   ├── exon3.bed.....................................................index
│   ├── intron.bed....................................................index
│   ├── splice_sites.csv...........................................validate
│   └── validated..................................................validate
│   └── events.csv.............................................validate
├── junctions.............................................................index
│   ├── metadata.csv......................................................index
│   └── reads.csv.........................................................index
└── psi.....................................................................psi
├── mxe.................................................................psi
| ├── psi.csv.........................................................psi
│   └── summary.csv.....................................................psi
├── outrigger_psi.csv...................................................psi
└── se..................................................................psi
├── psi.csv.........................................................psi
└── summary.csv.....................................................psi

10 directories, 26 files

.. _Outrigger: https://github.com/YeoLab/outrigger