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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

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RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format).

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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