Project directory structure

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Each ExpressionPlot project is kept in a specific directory structure. I organize my filesystem so all the projects are in the projects/ subdirectory of the ExpressionPlot root directory, but in theory you could keep them anywhere, since ExpressionPlot finds your project by looking in a datasets.txt file with all registered projects. This is a simple two-column TSV file. The first column is the short name for the project and the second is the full path to the project directory. The location of datatsets.txt can be found by running expressionplot-config DATASETS_FN. The default location is in the root directory of the ExpressionPlot installation.

Meta-files

A complete project would contain meta-files in the root project directory (which we'll call $ROOT in this file). These are described here.

Gene/Transcript-level files

ExpressionPlot looks for files in two different places describing gene/transcript levels. Two files are found in $ROOT/analysis/gene_levels/. The first, gene_levels.tsv gives the raw read counts and RPKMs of every gene in your annotation. It has the following fields:

cluster cluster
aliases aliases
chr chr
start start
end end
str str
len len
brain brain