deepTools cluster information?

Question

[mbk0asis]

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!

Answer 1

[Devon Ryan]

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.

[mbk0asis]

Thank you! I missed that one...

[Devon Ryan]

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

[1769mkc]

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?

[Devon Ryan]

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

[mbk0asis]

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

[1769mkc]

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