Question: Plot a dotted line to the start of the regions in computeMatrix, deepTools
0
gravatar for Sho
22 days ago by
Sho0
Sho0 wrote:

Hello,

I'm now dealing with ChIP-Seq data to make heatmaps using deepTools 3.5.

In the process of "computeMatrix", I know I can add a dotted line to indicate the end of the regions by adding "--sortUsing region_length". However, is there anyway I can add a dotted line to the start of the regions?

Thank you very much for your help.

tool chip-seq • 105 views
ADD COMMENTlink modified 18 days ago by Devon Ryan97k • written 22 days ago by Sho0
0
gravatar for Devon Ryan
18 days ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

If you use --referencePoint center then you will get a dotted line on both ends (otherwise at least one end will be vertically aligned across genes, making such a guide line unnecessary).

ADD COMMENTlink written 18 days ago by Devon Ryan97k

Thanks for your comment. Actually I used "--referencePoint center" option, but it gave me a dotted line only on the end of the regions as explained in the deepTools homepage.

The command I used was like this:

computeMatrix reference-point --referencePoint center -b 1000 -a 1000 -bs 10 -R *.bed --missingDataAsZero --sortUsing region_length -S *.bw -o *.gz

The regions I used were already sorted by size, long regions at the bottom and short regions on the top in heatmap to make a mountain shape (because the reference point is the center of the regions).

But so far, by using the command above, I can only plot a dotted line on the end of the regions. (only the right side of the mountain)

Is there anyway to visualize the both ends of the regions in heatmap? Thanks.

ADD REPLYlink modified 17 days ago • written 17 days ago by Sho0

You might check if there's a newer version. I recall implementing this in one of the later 3.4 releases. Perhaps this got broken in 3.5, in which case please make a bug report.

ADD REPLYlink modified 14 days ago • written 14 days ago by Devon Ryan97k
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