Hello everyone,
I have a question. I had a heatmap with deeptools and I wanted to extract that small heatmap with the genes that have more signal (as shown in the image). Can someone help me?
Thank you in advance
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biostarsb •
Run it again with the parameter --outFileSortedRegions myfile.bed . The genes you want should be in the first cluster that comes up (I assume you have run it with a --kmeans 4 ? )
then i can extract the list of genes from the bed file and run again the computeMatrix then plotheatmap ?
Thank you
Sure ..should work this way
but the bed contain all genes not only those with high signal, for me i need to extract only those with high signal to do again onther computeMatrix and plotHeatmap
if you run again the plotHeatmap function with the parameters --kmeans 4 --outFileSortedRegions mynewfile.bed then your new bed file "mynewfile.bed" that is generated will be split into 4 different clusters.
The genes you want are in the first cluster
You have a couple options. Firstly, you could save the sorted output from computeMatrix, gunzip it, take the top N lines, fix the header and then gzip it again (computeMatrix outputs a bit gzipped text file, where the first line is a header defining things like the matrix size and where samples are).
Perhaps a better options would be to use kmeans in plotHeatmap, pull out the BED regions for the preferred cluster and then run computeMatrix on that.
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