Readme file
This is a updating set of scripts that I've pulled together to attempt and make analysis easier.
Methylome work:
fastq > bismark outputs - use wgbs_se_pipeline_v0.4.sh:
USAGE: wgbs_se_pipelinev0.2.sh <rel. path to bismark genome folder> Example: wgbs_st_pipelinev0.2.sh Bd21.fastq ../brachy_genomes/Bd21Control Bd21
This will create a folder structure in the directory you are in that contains the fastq files, fastqc reports, trimmed + filtered reads, secondary fastqc reports, bismark outputs, and windowed/coverage/bed files for visualization and analysis.
How to setup:
execute in a directory containg: your fastq file C_context_window_SREedits.pl