Re: [Gmod-ajax] JBrowse scale tracks together

[Ke J. <bio...@gm...>]

My solution to the scaling problem was to scale them before JBrowse: when
converting BAM or whatever other format to BigWig I supplied a scaling
factor based on mapped reads. This way, for one experiment, all BigWig
coverage are "normalized" across the board. When viewing them as individual
tracks on JBrowse, you'll get a normalized view and could compare across
samples.

On Thu, Oct 25, 2018 at 12:29 PM Vaneet Lotay <van...@uc...>
wrote:

> Thanks for the tip, already have that plugin installed and it is the
> closest thing to my request so far.  However it would nice to just have it
> so that you can graph bigwigs in the traditional bigwig XY plot format.
> The multibigwig plugin does have an XYplot option but it has no legend for
> each track and graph color.  Also I mean to graph all tracks separately in
> their own track lines as opposed to graphing them all together on the same
> physical space.  This does work though as a good temporary measure until a
> new feature can be added to JBrowse.
>
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary AB T2N 1N4*
>
> *CANADA*
>
>
>
> *From:* Ke Jiang [mailto:bio...@gm...]
> *Sent:* Thursday, October 25, 2018 11:25 AM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse scale tracks together
>
>
>
> Would this help?
>
>
>
> https://github.com/elsiklab/multibigwig
>
>
>
> On Thu, Oct 25, 2018 at 12:10 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello all,
>
>
>
> I am wondering if there’s a feature or plugin in JBrowse that allows you
> to view bigwig tracks together in a group that will allow you to scale them
> together when viewing them in a browser.  When I say scale them together, I
> don’t necessarily mean they all have the same maximum value for their
> graphs, but that whichever scaling you choose (local, global, max,…) that
> it’s common among all tracks in the group.
>
>
>
> I think this is greatly needed because unless you set each bigwig track to
> the same maximum scale manually, comparing tracks together which are
> locally or globally scaled can be tough as more often than not they have
> different scales for their Y axes.
>
>
>
> So I’m not sure if there’s a way to make track groups like this for this
> purpose, if not, please add this request for the next JBrowse release if
> you feel this is necessary.
>
>
>
> I really appreciate you adding the sorting of track categories, so
> impressed with how quickly you guys post new JBrowse releases as well as
> adding user requests.  I wouldn’t really begin to know how you can add a
> feature for custom sorting tracks within a category, but would that be
> possible to add in a future release somehow? Maybe an orderID of some sort
> perhaps?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building – University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
>
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