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https://github.com/kdm9/rnaseqpipeline

Last synced: 11 days ago
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Host: GitHub
URL: https://github.com/kdm9/rnaseqpipeline
Owner: kdm9
Created: 2013-05-28T05:15:04.000Z (over 11 years ago)
Default Branch: master
Last Pushed: 2014-02-27T22:48:11.000Z (over 10 years ago)
Last Synced: 2024-10-11T19:23:01.465Z (about 1 month ago)
Language: Shell
Size: 740 KB
Stars: 0
Watchers: 1
Forks: 1
Open Issues: 1
Metadata Files:
- Readme: README.md

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README

        OVERVIEW

========

Bash script pipelines to complete an RNAseq differential expression analysis.

Each directory contains scripts with alternative implementations of various

parts of the pipeline. To run, create a script which `source`es the file

containing the implementation of each step you require, and run the function

with the step name. See example.sh for an example.

Developed by Kevin Murray (with contributions from Peter Crisp), 2013.

LICENSE

=======

Available under the GNU GPL v3 or later.

DESCRIPTION

===========

This is a work in progress

Steps:

- 01: quality control of raw reads (trimming, generation of QC reports, etc)

- 02: alignment of raw reads to reference (everything from raw reads to a bam alignment file)

- 03: post-processing of alignemnts (exracting counts, filtering alignments by arbirtary criteria, etc)

- 04: initial statistical analysis (normalisation, etc if required [may be done in 05])

- 05: differential expression analysis (statstical testing of differential expression)

- 06: post-analysis

There are also some misc scripts, such as index creation etc.

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