Re: [Gmod-ajax] Question from CSHL course participant

[Scott C. <sc...@sc...>]

Hi Gabriel,

I'm cc'ing the JBrowse mailing list in case anybody else from the community
wants to chime in. I'll try to address your questions inline below

On Wed, Oct 25, 2023 at 1:22 PM Barcia Durán, José Gabriel <
Gab...@ny...> wrote:

> Hi Scott,
>
>
> I'm an instructor at NYU Langone—the one who kept asking about JBrowse 2
> this afternoon. Thanks for your presentation; it was really useful.
>
>
> Thanks for saying so!


> I've been using IGV for years, so I'm quite please to learn there's a user
> friendly, more modern alternative.
>
>
> Would you mind clarifying a couple things for me?
>
>
> I'd use JBrowse 2 to visualize RNA-seq, ATAC-seq, ChIP-seq, and Hi-C data
> and produce figures for publication. It seems I'd only need to use the
> desktop tool—does that sound right?
>

Yes, anything that can be done in the web interface can be done with the
desktop tool as well, so if you're not interested in sharing the data on
the web (or not interested now--you can always decide to later!), the
desktop app should be fine. For RNA-seq, ATAC-seq and Chip-Seq, anything
that can be expressed either as a BAM/CRAM (for alignment) or as a BigWig
(for coverage, though the BAM/CRAM adapter can calculate coverage too) can
be displayed in JBrowse. I was about to write that Hi-C needed an external
plugin but I just checked one of my JBrowse instances and saw that it's
installed by default (I don't think it used to be). I don't have much
experience with that type of data, but there is a config guide for it on
the website:

  https://jbrowse.org/jb2/docs/config_guides/hic_track/

The "add track" dialog supports Hi-C data, so it should work in exactly the
same way as the example when I added a GFF file during the class.

>
> I am curious to be able to see the same genes in two species, with their
> associated data (e.g., RNA-seq), on different tracks but the same
> visualization. Would that be possible for human and mouse genes? Do I need
> a special config to be able to do this? I don't think I see the mouse
> genome come up in the available tracks on the right.
>

Yes, it is certainly possible. The JBrowse instance I'm creating for the
Alliance of Genome Resources will have that (ie, hg38 and mm39). You can
have multiple genomes displayed in a view. Not just with synteny views like
I showed in class, but two separate genomes can be displayed by using the
"Add" menu and selecting "Linear Genome View" which will give you a dialog
to pick another genome (or the same one, if you'd like to view to locations
of the same genome at once).  Here's an example from my dev JBrowse
instance--the only downside is that the mouse tracks are pretty barebones,
but you could always use the add tracks option to add your own :-)

https://stage.dgaayxgqoarxf.amplifyapp.com/?session=share-sZAZdFpp6d&password=fstZ2

Also, with the synteny view like this one:

https://stage.dgaayxgqoarxf.amplifyapp.com/?session=share-qiDQVIpEqW&password=iiukF

You can add any tracks you want to either the human or the mouse views, and
either ones that are provided with the browser or tracks of your own.
The glyph/button in the upper left corner that looks like three tiny
checkboxes with lines next to them will open the track selector for either
the upper or lower assembly.
The only caveat I have is that you might want to make sure you have a nice
tall browser because I have definitely turned my external monitor on its
side sometimes
to see all of the tracks I want to add :-)


> Lastly, I'm also interested in lncRNAs—is JBrowse a good tool to visualize
> those annotations? Would I be able to add my own annotations, in the event
> the transcripts I'm interested in are missing?
>

 As far as I know JBrowse is good a visualizing lncRNAs, but you tell me:

https://stage.dgaayxgqoarxf.amplifyapp.com/?session=share-IHNTRxxy_y&password=7Awgt

(I don't know a lot about lncRNAs either--to me it's just another gene type
with coordinates that I want to display. If there is something you think it
could do better to improve the expressiveness of the display, let me know!)

As for adding your own--it depends on what you mean and want to have
happen. If for example, you run an analysis or have predictions or the like
that indicate the presence of a lncRNA and you get those results in a
common format (GFF, Bed or GTF would be the most common examples), you can
use that to add a new track of "your" lncRNAs. If you want them displayed
in the same track as the annotations that come from the source (RGD for
human and MGI for mouse in the JBrowse links above), you would have to go
through a little more effort to merge the source GFF files and then
"re-add" them to JBrowse. Lastly, if you wanted to use a graphical editor
to create the gene annotations yourself, you'd have to go down the route of
getting Apollo, which is probably more work than you'd want to do depending
on the size of your project.

I hope this all at least makes some sense; please let us know if you have
more questions!

Scott


> Thanks again,
>
>
> Gabriel
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)