TAMA GO: Saturation Curves - GenomeRIK/tama GitHub Wiki

This tool in TAMA-GO is used to produce a saturation curve for gene discovery.

In order to run tama_sampling_saturation_curve.py, you will need to create a read support file for the annotation using tama_read_support_levels.py.

tama_sampling_saturation_curve.py

To produce a saturation curve for gene discovery use tama_sampling_saturation_curve.py.

usage: tama_sampling_saturation_curve.py [-h] [-r] [-b] [-o]

arguments:

  -h, --help  show this help message and exit
  -r R        Read support file
  -b B        Read bin size
  -o O        Output file name

Default command would look like this:

python tama_sampling_saturation_curve.py -r read_support.txt -b 10000 -o saturation_curve_histo.txt

Detailed explanation of arguments:

-r R

The readsupport file is the output file from running tama_read_support_levels.py.

-b B

Bin size for read counts.

-o O

This is the output file name.

Outputs:

  saturation_curve_histo.txt

Detailed explanation:

saturation_curve_histo.txt

This is a 2 column file with read count bin and number of genes detected.

An example:

  read_count      gene_count
  10000   5292
  20000   7937
  30000   9797
  40000   11274