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https://github.com/vimalkvn/riboplot
RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format).
https://github.com/vimalkvn/riboplot
bioinformatics bioinformatics-scripts ngs riboseq ribosome-profiling
Last synced: 2 months ago
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RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format).
- Host: GitHub
- URL: https://github.com/vimalkvn/riboplot
- Owner: vimalkvn
- License: bsd-3-clause
- Archived: true
- Created: 2015-08-19T11:16:54.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2018-08-04T21:42:15.000Z (about 6 years ago)
- Last Synced: 2024-07-01T18:34:05.597Z (3 months ago)
- Topics: bioinformatics, bioinformatics-scripts, ngs, riboseq, ribosome-profiling
- Language: Python
- Homepage:
- Size: 2.85 MB
- Stars: 4
- Watchers: 2
- Forks: 1
- Open Issues: 2
-
Metadata Files:
- Readme: README.rst
- Changelog: HISTORY.rst
- Contributing: CONTRIBUTING.rst
- License: LICENSE
Awesome Lists containing this project
- awesome-riboseq - Code
README
========
RiboPlot
========
.. image:: https://img.shields.io/pypi/v/riboplot.svg
:target: https://pypi.python.org/pypi/riboplot
RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format).
There are two programs in the package:
**riboplot**
Plot and output read counts (csv) for a single transcript.
**ribocount**
Output read counts for all transcripts in an alignment.
Quickstart
----------
Installation
............
riboplot can be installed easily with Conda_ using the command::
conda create -n riboplot riboplot
This is the **recommended** method. Please check the
installation_ section of the documentation for alternative
installation methods.
Get sample data
...............
For convenience, this repository includes sample Ribo-Seq and
RNA-seq data (from `Bazzini et.al`_) that have been processed
through the RiboGalaxy pipeline - removal of adapters and rRNA
followed by aligning the reads to the transcriptome. The resulting
alignment (SAM) file is then converted to BAM format which is
then sorted. If you would like to learn more about this workflow,
please check the `published page`_ on RiboGalaxy.
To get sample data, clone this repository::
git clone https://github.com/vimalkvn/riboplot
Activate the conda environment created above::
source activate riboplot
Change to the directory containing sample data::
cd tests/data
Plot and output Ribo-Seq read counts for a single transcript (riboplot)
.......................................................................
::
riboplot -b 5hRPFsorted.bam -n 5hmRNAsorted.bam \
-f zebrafish.fna -t "gi|41055123|ref|NM_201172.1|"
Here::
-b Ribo-Seq alignment file in BAM format
-n RNA-Seq alignment file (BAM)
(optional, for including RNA coverage in the plot)
-f FASTA format file of the transcriptome
-t Name of the transcript as in the FASTA file
Outputs will be in the *output* folder. Plot is saved as
*riboplot.png* and the read counts will be in *RiboCounts.csv*.
.. image:: docs/images/riboplot_default.png
:scale: 60 %
:alt: RiboPlot of a single transcript
Output read counts for all transcripts (ribocount)
..................................................
::
ribocount -b 5hRPFsorted.bam -f zebrafish.fna
When the run is complete, a zip file called
*ribocount_output.zip* will be created in the *output* folder.
Uncompress this file and open *index.html* in a browser::
cd output/
unzip ribocount_output.zip
cd ribocount_output/
xdg-open index.html
.. image:: docs/images/ribocount.png
:scale: 60 %
:alt: RiboCount of all transcripts
For detailed usage, please check the online documentation
http://pythonhosted.org/riboplot
PyPI: https://pypi.python.org/pypi/riboplot
Github Repository: https://github.com/vimalkvn/riboplot
Online: http://ribogalaxy.ucc.ie (under RiboSeq Analysis/RiboPlot)
Free software: GPL license.
.. Links
.. _Bazzini et.al: https://www.ncbi.nlm.nih.gov/pubmed/24705786
.. _Conda: https://conda.io
.. _installation: https://pythonhosted.org/riboplot/installation.html
.. _published page: https://ribogalaxy.ucc.ie/u/vimalkumarvelayudhan/p/using-riboplot-and-ribocount