Question: extract small heatmap from big one deeptools
1
gravatar for biostarsb
2.1 years ago by
biostarsb20
biostarsb20 wrote:

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)

someone can help me ?

thank you in advance

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chip-seq tools deeptools • 978 views
ADD COMMENTlink modified 2.1 years ago by Devon Ryan88k • written 2.1 years ago by biostarsb20

waiting for help !!!!!

ADD REPLYlink written 2.1 years ago by biostarsb20

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

Are you losing money by the minute here :-) It has been less than 30 min since you posted the original question.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by genomax64k

Tagging: Devon Ryan

ADD REPLYlink written 2.1 years ago by genomax64k
2
gravatar for Constantine
2.1 years ago by
Constantine220
USA
Constantine220 wrote:

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 ? )

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Constantine220

then i can extract the list of genes from the bed file and run again the computeMatrix then plotheatmap ?

Thank you

ADD REPLYlink written 2.1 years ago by biostarsb20

Sure ..should work this way

ADD REPLYlink written 2.1 years ago by Constantine220

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

ADD REPLYlink written 2.1 years ago by biostarsb20

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

ADD REPLYlink written 2.1 years ago by Constantine220
1
gravatar for Devon Ryan
2.1 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

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.

ADD COMMENTlink written 2.1 years ago by Devon Ryan88k
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