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GRPutils

This repository contains utilities to manipulate Artemis compatible coverage graphs (denote *.grp format), and a set of commands developed based on this file format. The grp file can be visualized using Artemis directly by clicking on Graphs => Add User Plot. The majority of the grp manipulating commands can be found within grptools.

  • wig2grp.py: convert Wiggle files generated by bam2wig.py from the RseQC package to grp format.
  • merge_grp.py: given a list of grp files from the same genome, this script will average/add-up the coverage at each genome coordinate, then return a new grp file.
  • grptools: a suite of subcommands for grp file manipulations.
  • tptools: a suite of subcommands for TSS prediction and classification.
  • tss_analysis_pipline.sh: an example shell script utilizing grptools and tptools for grp file processing, TSS prediction and classification.