/HexamerBias

Random hexamer bias analysis

Primary LanguagePython

Random hexamer bias analysis by Emma Dann

The most important folders (the ones that you will most likely have to use) are marked with a (!!!)

Contents

  • artificial_coverage: (!!!) building and analyzing predicted coverage profiles
  • base_composition: making profile of kmer content at specific genomic regions
  • BS_processing: wrappers to process raw reads (trimming, mapping, meth calling) for BS converted and not converted and multiple organisms
  • deltaGprediction: (!!!) scripts for prediction of binding energies from sequencing data
  • in_silico_conversion: scripts for in silico BS conversion of genome
  • optimization: (!!!) algorithm for primer batch optimization (implementation of Differential Evolution and E-score functions)
  • primer_concentration_effect: Analysis of differences in coverage for different primer batches.
  • quantify_bias: (!!!) analysis of experimental coverage profiles (in genes, sites of interest etc...)
  • rounds_preamp: analysis of effect of variable number of preamplification rounds
  • rscripts: miscellaneous r scripts
  • snakefile: tentative snakemake pipeline for Delta G prediction (not fully functional)
  • thrashNsnippets: old scripts and random stuff
  • utils: miscellaneous useful scripts (seq data handling, kmer counting, tests...)
  • hexVSprimed.py: miscellaneous helper functions for hexamer analysis scripts (not changing location not to mess up calling)