Updated: 07 April 2014 by Joy-El R.B. Talbot

Create custom plots that summarize read alignments patterns over user-defined genomic features. Requires alignment files (indexed BAM format) and feature files (currently BED or GFF format) which can describe any type of feature expressed by start and end chromosomal coordinates. Please see the USERS_GUIDE.md for more details and a list of metagene counting options.

1. python 2.7.x (https://www.python.org/downloads/)
2. samtools 0.1.18+ (http://sourceforge.net/projects/samtools/files/)
3. R 2.15.2 (http://cran.us.r-project.org/)

1. Unzip download from github
2. Make sure that samtools and R are in your $PATH
3. Start by running metagene_count.py (then metagene_bin.py, then your flavor of metagene_plot_*.py)

The initial step in metagene_analysis (metagene_counts.py) is based on original Perl code by Karl F. Erhard, Jr Copyright (c) 2011.

Joy-El R.B. Talbot Copyright (c) 2014

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