totalinfo

Contents

• totalinfo
  • Overview
  • Command-line usage
  • Example Input and Output

Overview

totalinfo is a program within the sortseq_tools package which calculates the mutual information between gene expression and knowledge of the entire sequence. This should be run on a sublibrary, which is a typical experiment, only run with only 200-300 unique sequences. The mutual information calculated represents the maximum amount of information acheivable by any model.

After you install `sortseq_tools`_, this program will be available to run at the command line.

Command-line usage

usage: sortseq totalinfo [-h] [-mpra REPORTERARRAY] [-o OUT]

Options:

-mpra=False, --ReporterArray=False
	Is the experiment a massively parallel reporter assay? Default=False
-o, --out	Undocumented

Example Input and Output

Example input table:

seq    ct_0    ct_1     ct_2
ACGGT  2000    1500     3000
AGGTT  100     4050     6500
...

Example Output Table:

MI    std
.805  .05