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deepTools cluster information?

Hi.

I generated a heatmap with several clusters using "deepTools" something like below, and I want to know the names of elements in each cluster. But, it seemed no tool existed among the "deepTools suit".

Can anyone help me?

Thank you!

enter image description here

deeptools kmeans clustering
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updated by Devon Ryan Devon Ryan • written by mbk0asis mbk0asis

1 answer

If you use the --outFileSortedRegions something.bed option then a BED file will be produced with a column noting the cluster that each gene/region/feature is in.

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written by Devon Ryan Devon Ryan

Thank you! I missed that one...

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written by mbk0asis mbk0asis

BTW, if you have the matrix that produces the behavior you described here then feel free to send it to me.

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written by Devon Ryan Devon Ryan

I have the same question , I used this argument "--outFileSortedRegions" i get output something like this

#chrom  start   end name    score   strand  thickStart  thickEnd    itemRGB blockCount  blockSizes  blockStart  deepTools_group
chr1    21357   21858   chr1:21357-21858    .   .   21357   21858   0   1   501 21355   genes
chr1    25092   25982   chr1:25092-25982    .   .   25092   25982   0   1   890 25090   genes
chr1    27280   27879   chr1:27280-27879    .   .   27280   27879   0   1   599 27278   genes
chr1    698092  698593  chr1:698092-698593  .   .   698092  698593  0   1   501 698086  genes
chr1    716292  716938  chr1:716292-716938  .   .   716292  716938  0   1   646 716285  genes
chr1    717990  718808  chr1:717990-718808  .   .   717990  718808  0   1   818 717983  genes

I do have chromosome then the coordinates but apparently the names of the genes are missing why is it?

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written by 1769mkc 1769mkc

DeepTools cares about regions so it will typically ignore their names, which tend to be non-existent.

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written by Devon Ryan Devon Ryan

As Devon Ryan mentioned, gene names won't be appeared in the result. You can annotate the regions with gene names using 'bedtools intersect'.

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written by mbk0asis mbk0asis

I did annotate it with homer ,but i will check out the "bedtools intersect'" how to annotate it

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written by 1769mkc 1769mkc

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