NormalizeTaxaTables#

Add to module run order:
#BioModule biolockj.module.report.taxa.NormalizeTaxaTables

Description#

Normalize taxa tables for sequencing depth.

Properties#

Properties are the name=value pairs in the configuration file.

NormalizeTaxaTables properties:#

none

General properties applicable to this module:#

Property Description
cluster.batchCommand string
Terminal command used to submit jobs on the cluster
default: null
cluster.jobHeader string
Header written at top of worker scripts
default: null
cluster.modules list
List of cluster modules to load at start of worker scripts
default: null
cluster.prologue string
To run at the start of every script after loading cluster modules (if any)
default: null
cluster.statusCommand string
Terminal command used to check the status of jobs on the cluster
default: null
docker.saveContainerOnExit boolean
If Y, docker run command will NOT include the --rm flag
default: null
docker.verifyImage boolean
In check dependencies, run a test to verify the docker image.
default: null
report.logBase string
Options: 10,e,null. If e, use natural log (base e); if 10, use log base 10; if not set, counts will not be converted to a log scale.
default: 10
script.defaultHeader string
Store default script header for MAIN script and locally run WORKER scripts.
default: #!/bin/bash
script.numThreads integer
Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter.
default: 8
script.numWorkers integer
Set number of samples to process per script (if parallel processing)
default: 1
script.permissions string
Used as chmod permission parameter (ex: 774)
default: 770
script.timeout integer
Sets # of minutes before worker scripts times out.
default: null

Details#

version: 1.0.0

Normalize taxa tables based on formula:

Where:

  • = raw count; the cell value before normalizing
  • = number of sequences in the sample (total within a sample)
  • = total number of counts in the table (total across samples)
  • = total number of samples

Typically the data is put on a scale, so the full forumula is:

The values will be in output dir of the LogTransformTaxaTables module. The values will be in the output of the NormalizeTaxaTables module.

For further explanation regarding the normalization scheme, please read The ISME Journal 2013 paper by Dr. Anthony Fodor: "Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model"

If report.logBase is not null, then the LogTransformTaxaTables will be added as a post-requisite module.

Adds modules#

pre-requisite modules
pipeline-dependent
post-requisite modules
biolockj.module.report.taxa.LogTransformTaxaTables

Docker#

If running in docker, this module will run in a docker container from this image:

biolockjdevteam/biolockj_controller:v1.4.2

This can be modified using the following properties:
NormalizeTaxaTables.imageOwner
NormalizeTaxaTables.imageName
NormalizeTaxaTables.imageTag

Citation#

"Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model"
Module developed by Mike Sioda.