CEGRcode/scriptmanager

Calculate scaling factor by regions (NFR normalization)

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owlang commented

Describe tool

NFR normalization scaling factors for genomic ChIP-exo data is based on an annotated set of regions that are expected to contain only background signal. The scaling factor is determined to be the value that scales the dataset such that the background region tag counts average to one arbitrary unit per base pair.

Implementation

This tool will be generalized to allow users to provide any set of "background regions" as a BED file, tag pileup, average the matrix values, and return the scaling factor for each input BAM file.

Recycle code from TagPileup to support different tag encodings.

Checklist

New tools should be written on branches off dev. A pull request to the dev branch can then be submitted and a reviewer will review the code and accept the merge.

  • Write tests
  • Write tool (list changed files)
    • objects.ToolDescriptions.java
    • scripts.MyTool.java
    • cli.MyToolCLI.java
    • window_interface.MyToolWindow.java
    • window_interface.MyToolOutput.java
    • main.ScriptManagerGUI.java
    • main.ScriptManager.java
  • Add logging support
  • Update documentation (docusaurus)
  • Write Galaxy wrapper

Then you can pull your changes into master! 🎉