bedGraph2Cluster

MATLAB Function for the k-Means Clustering of ChIP-seq bedGraph Data

MATLAB_VERSION	RUNTIME_VERSION
R2018b	9.5

bedGraph2Cluster(bedGraphs_Signal, bedGraphs_Control, bedGraphs_Cluster, bedGraphs_Heatmap, outdir, bed_bin, fold_change, normalization_method, k, distance_method, clustering_method, workingdir)

Required arguments

bedGraphs_Signal (string): comma-delimited list of bedGraph files to be included during peak calling

bedGraphs_Control (string): comma-delimited list of bedGraph files to be used as controls for peak calling

bedGraphs_Cluster (string): comma-delimited list of bedGraph files to be included during k-means clustering

bedGraphs_Heatmap (string): comma-delimited list of bedGraph files to be included in heatmap

outdir (string): path to the output directory

bed_bin (string): path to the BED file used for binned bedGraph generation

fold_change (string): threshold for the fold change over the control during peak calling

normalization_method (string): normalization method to utilize ("QNorm": QNorm, "CPM": CPM)

k (string): number of clusters during k-means clustering

distance_method (string): distance metric for k-means clustering ("sqeuclidean", "cityblock", "cosine", "correlation")

clustering_method (string): clustering method to utilize ("1": profile, "2": profile+scalar, "3": symmetry_collapsed_profile+scalar)

Optional arguments

workingdir (string): path to the output directory

Output files

tiles_200_data.mat: MATLAB variable for the entire dataset

tiles_200_data_peak.mat: MATLAB variable for only the peakset

peaks.bed: BED file of the peakset

peaks.clust${k}.${clusterID}.bed: BED file of the peakset for each cluster

clustering_heatmap.pdf: heatmap for the k-means clustering

Examplary usage

with license for MATLAB

bedGraph2Cluster("bedgraph/RB.WT.bedgraph,bedgraph/RB.dCDK.bedgraph", "bedgraph/INPUT.WT.bedgraph,bedgraph/INPUT.dCDK.bedgraph", "bedgraph/RB.WT.bedgraph,bedgraph/RB.dCDK.bedgraph,bedgraph/H3K4me3.WT.bedgraph,bedgraph/H3K4me3.dCDK.bedgraph,bedgraph/H3K4me.WT.bedgraph,bedgraph/H3K4me.dCDK.bedgraph,bedgraph/H3K27ac.WT.bedgraph,bedgraph/H3K27ac.dCDK.bedgraph", "bedgraph/RB.WT.bedgraph,bedgraph/RB.dCDK.bedgraph,bedgraph/H3K4me3.WT.bedgraph,bedgraph/H3K4me3.dCDK.bedgraph,bedgraph/H3K4me.WT.bedgraph,bedgraph/H3K4me.dCDK.bedgraph,bedgraph/H3K27ac.WT.bedgraph,bedgraph/H3K27ac.dCDK.bedgraph,bedgraph/E2F1.bedgraph,bedgraph/CTCF.shSCR.bedgraph,bedgraph/c-Jun.shSCR.bedgraph", "output", "bed/hg19.200bp.bed", "2", "true", "8", "cosine", "1", "../")

without license for MATLAB

pip3 install run_matlab
run_matlab install -v R2018b -r 9.5
git clone https://github.com/hanjunlee21/bedGraph2Cluster
run_matlab run -v R2018b -r 9.5 bedGraph2Cluster bedGraph2Cluster bedgraph/RB.WT.bedgraph,bedgraph/RB.dCDK.bedgraph bedgraph/INPUT.WT.bedgraph,bedgraph/INPUT.dCDK.bedgraph bedgraph/RB.WT.bedgraph,bedgraph/RB.dCDK.bedgraph,bedgraph/H3K4me3.WT.bedgraph,bedgraph/H3K4me3.dCDK.bedgraph,bedgraph/H3K4me.WT.bedgraph,bedgraph/H3K4me.dCDK.bedgraph,bedgraph/H3K27ac.WT.bedgraph,bedgraph/H3K27ac.dCDK.bedgraph bedgraph/RB.WT.bedgraph,bedgraph/RB.dCDK.bedgraph,bedgraph/H3K4me3.WT.bedgraph,bedgraph/H3K4me3.dCDK.bedgraph,bedgraph/H3K4me.WT.bedgraph,bedgraph/H3K4me.dCDK.bedgraph,bedgraph/H3K27ac.WT.bedgraph,bedgraph/H3K27ac.dCDK.bedgraph,bedgraph/E2F1.bedgraph,bedgraph/CTCF.shSCR.bedgraph,bedgraph/c-Jun.shSCR.bedgraph output bed/hg19.200bp.bed 2 true 8 cosine 1 $PWD

BED_Bin

hg19: https://drive.google.com/uc?id=1chMyuUAK3rycgAbj1P-FnWhJkW7K0q0H&export=download&confirm=t

hg38: https://drive.google.com/uc?id=1kfVOx78xTBoJHC7EL_HnkCFiWxdrNDal&export=download&confirm=t

Examplary output

All output files

Clustering heatmap

k=3	k=8