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template.cfg
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template.cfg
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# This is an example of a config file for C3D
# Usage: sh path/to/c3d.sh <config file>
# Parameters for config file
# reference (Optional if matrix provided)
# Reference sample BED/BEDGRAPH
# testAnchors (Required)
# File with anchor regions BED (chr,start,stop,gene)
# db (Optional if matrix provided)
# File containing list of background files BEDGRAPH
# outDirectory (Required)
# Output directory
# matrix (Optional if reference and db provided)
# Signal data with regions as rows & samples as columns. It must have row names in chr:start-end format. If not provided, a matrix will be generated using reference & db
# window (Optional)
# Number of flanking bps from anchor to check for open regions. If set to genome, it will take the correlation between each anchor DHS & every DHS in the reference. Defaults to 500000
# correlationThreshold (Optional)
# Correlation threshold. Only interaction candidates with correlations above or equal to this will be shown. Defaults to 0.7
# pValueThreshold (Optional)
# P-value threshold. Only interaction candidates with p-values below or equal to this will be shown. Defaults to 0.05
# qValueThreshold (Optional)
# Q-value threshold. Only interaction candidates with q-values below or equal to this will be shown. Defaults to 0.1
# correlationMethod (Optional)
# Correlation coefficient (pearson, spearman, kendall). Defaults to pearson
# figures (Optional)
# y if figures should be generated. Leave this parameter out if you do not want figures
# figureWidth (Optional)
# Number of flanking bps from anchor to display on figures. Use a comma-separated list to assign different widths to different figures. For example, if you have 3 figures and 500000,100000,400 is passed then the figures will show 500000, 100000, and 400 bps around the first, second, and third anchors respectively. Defaults to window
# zoom (Optional)
# Number of flanking bps from anchor to show for zoomed figures. You can also pass a comma-separated list of numbers if you want different zoom regions for each figure. For example, if you have 3 figures and you pass 10000,50000,75000 then the zoom regions for figures 1,2, and 3 will be 10000,50000, and 75000 respectively. Use 0 if you do not wish to zoom. Defaults to no zoom
# colours (Optional)
# 4 colours for the interaction plots. For example, if blue,red,green,purple is passed then arcs of interactions with q-values>0.05 will be blue, between 0.05 and 0.01 will be red, 0.01 and 0.001 will be green and below 0.001 will be purple. Hexadecimal digits accepted. Defaults to shades of blue
# tracks (Optional)
# y if a file with tracks should be generated. This file can be uploaded to the UCSC Genome Browser to view interaction candidates. It creates the file by default. Change this parameter to anything but y if you do not want the file
# assembly (Optional)
# reference genome of the reference and db files. Defaults to hg19
# Multi-sample Parameters:
# Do not include reference or matrix if you want to run C3D on multiple samples"
# references (Optional if matrices provided)
# A file containing a list of reference sample BED/BEDGRAPHs where each line is of the form '<reference.bed> <sample name>'.
# matrices (Optional if references and db provided)
# A file containing a list of reference sample matrices where each line is of the form '<signalMatrix.txt> <sample name>'.
# All other parameters are available
# C3D will only read lines which contain "module load" or equal signs
# This is how variables are set. Note that there are no spaces in variable names, values or around equal signs.
reference=<path/to/reference.bed>
db=<path/to/list_of_bedgraphs.txt>
testAnchors=<path/to/anchors.bed>
outDirectory=<path/to/output>
matrix=
window=500000
correlationThreshold=0.7
pValueThreshold=0.05
qValueThreshold=0.05
correlationMethod=pearson
figures=n
figureWidth=500000
zoom=100000
colours=red,blue,green,purple
tracks=n
assembly=hg19
references=
matrices=