config-setup.txt

## =============== ##
##   CONFIG FILE   ##
## =============== ##

# This file consists of variables one needs to change to suit their dataset
# It mainly consists of file paths and data specific features. Some defaults
# are given for you, but please check all entries.

## --------------- ##
## GLOBALLY NEEDED ##
## --------------- ##

# Full file path to the root of this repository.
# Ensure to surround in quotes
REPO_DIR=""

# Base directory to send processed data to.
BASE_DIR=""

cell_type="bulk"

# Full file path to conda.sh found in your conda's installation directory
# specifically in path/to/conda/etc/profile.d/conda.sh
CONDA_SHELL=""

## -------------- ##
## ONT AND BS-SEQ ##
## -------------- ##

# Bed file locations
ONT_bed_file_location=
WGBS_bed_file_location=
oxBS_bed_file_location=

# See README.md for details
CPG_ISLANDS_REFERENCE="${REPO_DIR}/references/cpg_islands_hg19.bed.gz"

# Thresholds on the read depth considered for filtering input bed files
# Max read depth is included due to 
# [this paper](https://doi.org/10.1186/s13059-024-03207-9)
# If you don't believe this finding, just set this to be a really big number.
minimum_read_depth=30
maximum_read_depth=10000

# Thresholds for creating 'good reference datasets' for obtaining value of p
# that is used in binomial distribution (look at README.md for more info)
# This is split into thresholds for 5mC and 5hmC as 5hmC usually has lower
# read depth and less sites at high levels of hydroxymethylation (for ONT data).
reference_read_depth_threshold_m=50
reference_percentage_threshold_m=5
reference_read_depth_threshold_h=50
reference_percentage_threshold_h=5

# Default is very strict, loosen this if you want a more lax definition of 
# '(hydroxy)methylated'
binomial_threshold=1.7e-8

# This is the bin size that will be used by ChromHMM. Ensure you use the same
# value when using ChromHMM. (ChromHMM default is also 200bp)
BIN_SIZE=200

# file path to chromosome sizes for assembly.
# This file is expected to be of the form "chromosome \t size"
# These files are included in the installation of ChromHMM, not using these
# files might cause some errors.
chromosome_sizes=

# single quoted value
# m -> methylation, h -> hydroxymethylation
mark="m"

# Specifically for extracting 5hmC, this is the significance level to use with
# confidence intervals. Please see README.md for more information.
# WARNING: Going for anything more strict than a 99% confidence interval will
# result in zero hydroxymethylation signal unless you have very high average
# read depth.
significance_level=0.05

# The threshold used by the beta distribution when determining densely
# methylated bins
beta_threshold=0.001

## --------------------- ##
## CHIP_SEQ BINARIZATION ##
## --------------------- ##

# This will appear as the epigenetic mark name in the resultant binary file
epigenetic_mark_name=
input_MACS_file=


## ------------- ##
## SUPPLEMENTARY ##
## ------------- ##

# bed file you wish to analyse further in supplementary scripts
bed_file_location="${ONT_bed_file_location}"

## ......................... ##
##   Plotting error rates    ##
## ......................... ##

# In some datasets, the maximum value for the read depth of a single site
# can be in the thousands. However, most sites are well below this number,
# putting a maximum value here helps with interpretability of plots.
max_N_value=750

## .................. ##
##   CpG robustness   ##
## .................. ##

# Minimum distance between CpGs that you would consider 'close proximity'
min_distance=0

# Maximum distance between CpGs that you would consider 'close proximity'
max_distance=30

## ============== ##
##   PARAMETERS   ##
## ============== ##

# Ideally these don't need to be touched. You can change them if you wish
# however.

LOG_DIR=${BASE_DIR}/LogFiles
RSCRIPT_DIR="${REPO_DIR}/Rscripts"
FUNCTIONS_DIR="${REPO_DIR}/functions"
AWK_DIR="${REPO_DIR}/AWKscripts"
BINARY_DIR="${BASE_DIR}/BinaryFiles"

# Change to 1 to keep certain intermediate files and print debug logs
DEBUG_MODE=0