CCPipeline: CCPipeline

In WHG1990/CCTools: A suite of tools for analysing CC-seq data.

CCPipeline

Description

Inputs the "Molecule" files in generated in the "Analysis" folder by termMapper. Outputs whole genome "FullMap" files for each sample, with and without de-duplication (based identical R1&R2 coordinates between independent molecules). Also outputs histograms plots which detail the degree of PCR duplication in the each sample. Also outputs a "DSBList" (list of all FUllMaps), in RDS format.

Usage

CCPipeline(
  work.d,
  exp.name,
  combine = T,
  readMidpoint = F,
  subsamplereads = F,
  R2Map = F
)

Arguments

work.d	location of the desired working directory.
exp.name	name of the rds file generated.
readMidpoint	Do you want to call the midpoint of the molecule
subsamplereads	Do you want to subsample. For example enter 0.5 to sub sample by 50 percent
R2Map	Do you want to generate a R2 map

Author(s)

Will Gittens George Brown

WHG1990/CCTools documentation built on June 16, 2024, 1:36 a.m.