modeling_h1ddm1

bisulfite sequencing processing from
raw fastq to window-by-annotation style output

steps:


demultiplex

trim-galore

map with bsmap

compute per-base methylation score with bsmap's methratio.py

calculate average TE methylation score with
make_wba_from_bsmap_output.sh

massage data in R using "processing_TEs" scripts and shell, producing 2 tables:

per-TE mCG per genotype and per-TE C+T (alongwith TE length) as coverage proxy