Re: [Gmod-ajax] quantitative ("wiggle") tracks do not work

[Mitch S. <mit...@be...>]

Look in your JBrowse instance at chr05 around base 15377500:

http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html?loc=chr05:15373621..15382921

Currently, JBrowse plots wiggle data on a linear scale, and by default
it uses the largest values in the wiggle file to define the top of the
plotted range. You have seen blank-looking images in the places you've
looked because most of your data values are much, much lower than the
maximum values in your dataset. They're so small in the plot that they
don't show up at all.

Right now, one thing you could do is add a --min and --max parameter to
the wig-to-json.pl command line to specify the range of values to plot.
For example, if you specified --min 0 --max 100 then the plot would show
values in that range, and values larger than that would be out-of-range
above the plot.

We've also been talking about adding an option to plot on a logarithmic
vertical scale; would that work for your data? I've looked at histograms
of some next-gen coverage data, and it seems like the distribution of
data values makes sense to plot on a logarithmic scale. But I think the
range of values that is most interesting depends on the biology, and
possibly on how the data is normalized; are you comparing this data to
some kind of control?

Regards,
Mitch

Lianfeng GU wrote:
> Hi prof Mitch:
>
> Thank you for your reply.
>
> After type "make" command in JBrowse root directory
>
> i run "bin/wig-to-json.pl --wig dataset/wig/Col.wig", however i cannot
> see any figure in Col.wig track.
>
> You can check it by following website:
>
> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html

[removed username and password because I'm cc-ing the mailing list. -Mitch]

> When i use your test dataset, the quantitative ("wiggle") tracks work
> well. You can see the Figure in wiggle tracks you can see it by
> following website:
>
> http://bioinfo.genetics.ac.cn/tool/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>
> The file of my Col.wig look like this:
>
> track type=bedGraph name="TopHat - read coverage"
> chr04 0 4051 0
> chr04 4051 4088 1
> chr04 4088 4090 14
> chr04 4090 4093 18
> chr04 4093 4094 20
> chr04 4094 4095 22
> chr04 4095 4096 24
> chr04 4096 4097 25
> chr04 4097 4126 28
> chr04 4126 4130 27
> chr04 4130 4153 28
> chr04 4153 4163 29
> chr04 4163 4165 16
> chr04 4165 4168 12
> chr04 4168 4169 10
>
> I donot know the reason that i cannot get any figure in wiggle tracks.
>
> Thank you for your suggestion and help.
>
> Best wishes
>
> Lianfeng
>
>
>
>