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Plot a dotted line to the start of the regions in computeMatrix, deepTools

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.

chip-seq
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updated by Ram Ram • written by Sho • Sho

1 answer

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).

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written by Devon Ryan Devon Ryan

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.

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written by Sho • Sho

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.

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written by Devon Ryan Devon Ryan

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