https://github.com/tomwhite/misp-2017

MISP camp 2017 materials and code
https://github.com/tomwhite/misp-2017

bioinformatics data data-visualization hackathon

Last synced: 2 months ago
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MISP camp 2017 materials and code

• Host: GitHub
• URL: https://github.com/tomwhite/misp-2017
• Owner: tomwhite
• Created: 2017-12-01T17:14:10.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2017-12-20T15:32:32.000Z (over 8 years ago)
• Last Synced: 2025-01-17T21:43:52.246Z (over 1 year ago)
• Topics: bioinformatics, data, data-visualization, hackathon
• Language: Python
• Homepage:
• Size: 641 KB
• Stars: 0
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
# MISP Camp 2017

This repo contains some of the code developed by Group A during MISP Camp 2017 in Denmark.

## Getting Started with Spark

This project has a few examples of how to use [Apache Spark](https://spark.apache.org/).

It is designed to be used with [Cloudera Data Science Workbench](https://www.cloudera.com/documentation/data-science-workbench/latest/topics/cdsw_overview.html).

See _word_count.py_ and _tips.r_ for examples.

## Data analysis of Chikungunya Defective Genomes

See _del.py_ and _entropy.py_. Also, _norm.sh_ for producing rough normalization read counts.

The following two images show the distribution of deletion start position across the genome. Note that for passage 2 deletions start in all gene regions, while by passage 12 deletions are not found in structural genes.

![Passage 2](images/passage2.png)

![Passage 12](images/passage12.png)

The following shows the distribution of GC bases across the genome.

![GC distribution](images/gc.png)

Finally, this diagram shows how normalized Shannon entropy varies by passage and replicate. There is a general downward trend to lower entroy states (more ordered), with some oscillation.

![Entropy](images/entropy.png)