Output kmeans clusters

[giardine]

deeptools 3.5.1 Python 2.7.5

computeMatrix reference-point -R h3SummMerged.bed -S $h3bbws -o matrixH3.gz --outFileNameMatrix matrixH3.tsv --outFileSortedRegions sortedPeaksH3.bed --upstream 1000 --downstream 1000 --binSize 10 --blackListFileName blacklist.bed --samplesLabel $labels3b --referencePoint center plotHeatmap -m matrixH3.gz -o metaHeatmapH3.pdf --kmeans 3 --colorMap coolwarm

The heatmap is generated successfully. The problem is that sortedPeaksH3.bed does not include the cluster numbers. How do I know which regions are in each cluster?

#chrom start end name score strand thickStart thickEnd itemRGB blockCount blockSizes blockStart deepTools_group chr2L 2502 2767 chr2L:2502-2767 . . 2502 2767 0 1 265 2500 genes

Thanks, Belinda

[JSegueni]

Hi, When plotting your heatmap, you can output the regions using the --outFileSortedRegions option. You will get an output file with the deepTools_group identifying the clusters.

Best, Julie.