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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.

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

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.