[maker-devel] representing gene tracks in gbrowse

[Shane Brubaker]

Thanks Scott.  I added a line "cache time = 0" to my conf file

I tried the glyph = gene.

I think it is working now!

I did have some strange behavior (or you could just call it confusion on my part) with updating the images.  I had also tried using the little question mark next to the track to change the shapes/colors, and I noticed that I had to go back and restore the defaults here, after loading into a new page.  I also added a line that says
sub_part = exon, I'm not sure if that helped.

So just for reference here is my track configuration now:

[Genes]
feature = gene
glyph = gene
base = 1
sub_part = exon
fgcolor = blue
height = 5
linewidth = 2
key  = Named gene


It now shows my gene track in the expected way.  Thanks very much for your help!!



________________________________________
From: Scott Cain [scott at scottcain.net]
Sent: Tuesday, October 13, 2009 12:25 PM
To: Shane Brubaker
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] representing gene tracks in gbrowse

Hi Shane,

Please keep your responses on the list, so everyone can see the
discussion.

First, I missed the part about it not changing (which, I realize, was
a pretty important part of the email).  You need to make sure that you
set "cache time    = 0" in your configuration file, or GBrowse will
used a cached image, not realizing you changed the conf file.  It
doesn't use the cached image when you change the track key, because
that is part of how it looks up the image.

For the data you sent me, you should be able to use the gene glyph,
which is a little better than related transcript glyphs, since it
knows how to deal with splice variants.

Scott


On Oct 13, 2009, at 2:26 PM, Shane Brubaker wrote:

> Hi, can someone recommend for me the proper way to configure a
> gbrowse track for the display of maker genes?
>
> I am running maker and producing gene models from augustus and
> snap.  I then load the data into chado.  This produces a feature for
> an mRNA with a polypeptide, and exons.
>
> No matter what I do to change the track configuration, I see a solid
> block instead of seeing the exons represented explicitly as in a
> typical gene model.  However my "protein_matches" track does appear
> segemented when I change the glyph to segments.
>
> In fact it is a bit strange, when I change the color or height I
> don't really see any change ... but if I change the key for example
> I will see the change when I refresh.
>
> Can anyone tell me the proper way to configure the track?
>
> Here is my current configuration:
>
> [Genes]
> feature = gene
> glyph = transcript
> base = 1
> ignore_sub_part = CDS intron
> fgcolor = blue
> height = 15
> linewidth = 2
> key = Named gene
>
>
>
> Thanks for your help.
>
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-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient.  Any review, copying, or distribution of this email (or any attachments thereto) by others is strictly prohibited.  If you are not the intended recipient, please contact the sender immediately and permanently delete the original and any copies of this email and any attachments thereto.