Question: deepTools cluster information?
1
gravatar for mbk0asis
2.8 years ago by
mbk0asis470
Korea, Republic Of
mbk0asis470 wrote:

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

clustering kmeans deeptools • 1.7k views
ADD COMMENTlink modified 2.8 years ago by Devon Ryan92k • written 2.8 years ago by mbk0asis470
8
gravatar for Devon Ryan
2.8 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

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.

ADD COMMENTlink written 2.8 years ago by Devon Ryan92k

Thank you! I missed that one...

ADD REPLYlink written 2.8 years ago by mbk0asis470

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

ADD REPLYlink written 2.8 years ago by Devon Ryan92k

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?

ADD REPLYlink written 28 days ago by krushnach80630
1

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

ADD REPLYlink written 28 days ago by Devon Ryan92k
1

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

ADD REPLYlink written 21 days ago by mbk0asis470

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

ADD REPLYlink written 21 days ago by krushnach80630
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