#This text file is the configuration file we used for our analyses. To generate valid pairs file, we use the scripts of an existing pipeline "Micro-Capture-C (MCC)" that is available for download at Oxford University Innovation Software Store. Further information of the pipeline is available at  http://www.jdavieslab.com/Code.html. The configuration file is uploaded here as MicroC_analysis.txt


##########################################################################################
#!/bin/bash

# This part of the script allows you to run the pipe by executing the config.txt file
perl /user/scripts/MicroC-analysis_pipeline_part1.pl -q -i ${0##*/}
exit

##########################################################################################
# Specifications 
##########################################################################################
# Insert path to the scripts /user/scripts
master_folder=

# Insert path that leads to genome_sizes.txt files
bigwig_folder=

# Insert the path for bowtie 2 to use for the reference genome
bowtie_genome_path=

# Insert the build of the genome you are using 
genome=

##########################################################################################
# File specifications
##########################################################################################

# NB the files must be named (filename)_R1.fastq   (filename)_R2.fastq - specify the (filename) - without the _R1.fastq
# Use fastq not fq
# Avoid special characters in the filenames such as additional "."s or spaces

file=

reference=

# The oligo file is a list of chrV-X of the yeast genome
oligo_file=

# Bed file specifying the color of the targets - must be in 8 column bed format with colour in the 8th column (r,g,b format)
colour_file=

##########################################################################################
# Parts of the first pipeline to run
##########################################################################################
trim_galore=Y
flash=Y
fq2fa=Y
blat=Y

splitter=Y

clean_wig=N
gunzip=N
gzip=N

##########################################################################################
# Parts of the second pipe parameters
##########################################################################################
Pipe2=Y

bowtie=Y
sort=Y
MCCanal=Y
postgzip=N
track_hub=Y
samtobam=N
macs2=Y