<p>Figure from this <a href="https://www.embopress.org/doi/pdf/10.15252/embj.201591279" rel="nofollow noreferrer">paper</a> which shows a profile plot in figure4 first figure.
<a href="https://i.sstatic.net/sASxO.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/sASxO.png" alt="figure" /></a>.This i guess is made using deeptools perhaps. Meanwhile</p>
<p>When i tried to do similar plot <a href="https://i.sstatic.net/C4awO.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/C4awO.png" alt="figure 2" /></a> the scale doesn't start from 0. So my question how did they set the scale from 0 or the data is as such in other words their data point starts from 0. In my case it starts above 0. So is there a way to scale or normalize to make it start from 0 as i see in the embo paper or its just the characteristics of the data itself generated.</p>

CC BY-SA 4.0
2020-12-01T21:38:09.543Z
lol.. your sequencing coverage is super high i guess, such that the average coverage across the genome, even for your control is 10 reads per million? i cannot see a y-axis label
StupidWolf
CC BY-SA 4.0
2020-12-01T23:57:20.150Z
and did you flip the samples? I think you should not bring it to zero.. it is what it is. If your control is a chip input, this is what I would expect. Note the example you showed above, it is a KO.
StupidWolf
CC BY-SA 4.0
2020-12-02T07:10:00.513Z
"and did you flip the samples?" that mystery haunts me since I'm the end guy in the chain it our collaborator who are might have jumbled up the samples i have checked  quite  number of times regarding the sample labeling im sure im running the samples as provided.
kcm
CC BY-SA 4.0
2020-12-02T07:11:25.337Z
"f your control is a chip input, this is what I would expect." Its the  WT ,h2bub chip of control sample
kcm
CC BY-SA 4.0
2020-12-02T09:32:39.990Z
yes for my plot the color are fine ..my doubt was regarding if the scale can be set to zero which i understand is a bad idea
kcm
CC BY-SA 4.0
2020-12-02T09:38:20.307Z
yeah you should not.. maybe use a zscale for the axis. Like convert your coverage to a zscale for each gene, take average z scores across all genes and plot that
StupidWolf
CC BY-SA 4.0
2020-12-02T09:38:45.467Z
you should see a flat line around 0 for your control and a bump for your chip
StupidWolf
CC BY-SA 4.0
2020-12-02T09:52:23.147Z
"maybe use a zscale for the axis. Like convert your coverage to a zscale for each gene, take average z scores across all genes and plot that " it can be done with deeptools or something else required?
kcm
CC BY-SA 4.0
2020-12-02T11:03:07.250Z
i code it from scratch.. you can maybe use https://deeptools.readthedocs.io/en/3.0.0/content/tools/computeMatrix.html and just scale the rows
StupidWolf
<deeptools>
Setting scale of profile plot from zero for chip seq profile plot
# Setting scale of profile plot from zero for chip seq profile plot

(Asked by: username_0 on 2020-12-01)

Figure from this [paper](https://www.embopress.org/doi/pdf/10.15252/embj.201591279) which shows a profile plot in figure4 first figure.
[![figure](https://i.sstatic.net/sASxO.png)](https://i.sstatic.net/sASxO.png).This i guess is made using deeptools perhaps. Meanwhile

When i tried to do similar plot [![figure 2](https://i.sstatic.net/C4awO.png)](https://i.sstatic.net/C4awO.png) the scale doesn't start from 0. So my question how did they set the scale from 0 or the data is as such in other words their data point starts from 0. In my case it starts above 0. So is there a way to scale or normalize to make it start from 0 as i see in the embo paper or its just the characteristics of the data itself generated.

**Tags:** deeptools
> **Comments:**
> **username_1**: lol.. your sequencing coverage is super high i guess, such that the average coverage across the genome, even for your control is 10 reads per million? i cannot see a y-axis label  
> **username_1**: and did you flip the samples? I think you should not bring it to zero.. it is what it is. If your control is a chip input, this is what I would expect. Note the example you showed above, it is a KO.  
> **username_0**: "and did you flip the samples?" that mystery haunts me since I'm the end guy in the chain it our collaborator who are might have jumbled up the samples i have checked  quite  number of times regarding the sample labeling im sure im running the samples as provided.  
> **username_0**: "f your control is a chip input, this is what I would expect." Its the  WT ,h2bub chip of control sample  
> **username_0**: yes for my plot the color are fine ..my doubt was regarding if the scale can be set to zero which i understand is a bad idea  
> **username_1**: yeah you should not.. maybe use a zscale for the axis. Like convert your coverage to a zscale for each gene, take average z scores across all genes and plot that  
> **username_1**: you should see a flat line around 0 for your control and a bump for your chip  
> **username_0**: "maybe use a zscale for the axis. Like convert your coverage to a zscale for each gene, take average z scores across all genes and plot that " it can be done with deeptools or something else required?  
> **username_1**: i code it from scratch.. you can maybe use https://deeptools.readthedocs.io/en/3.0.0/content/tools/computeMatrix.html and just scale the rows  

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## 0 answers

