gmod-ajax — JBrowse list

Re: [Gmod-ajax] Wiggle Tracks in JBrowse

[Ian H. <ih...@be...>]

Hi Andrew,

The logarithmic nature of zoomlevels means that the disk usage is 
dominated by the highest zoomlevel (one base per pixel). So changing the 
number of pre-rendered zoomlevels won't help too much.

For a ~3.2 gigabase genome, it does not seem totally out of whack for an 
image track (such as a wiggle track) to require 10 gigabytes of storage. 
That's about 3 bytes/base. I would expect of order 2 bytes/base (the 
highest zoomlevel you expect ~1 byte/base; the factor of 2 is about what 
you get from the geometric series corresponding to the sum over 
zoomlevels).  A bit more due to filesystem cruft.

So 3 bytes/base is not too bad... *if* the wiggle plot is purely random. 
If it's nonrandom, e.g. if it contains big swathes of nothing, then it 
should be possible to compress it much better than that - although we 
haven't really played with the compression too much.

Bottom line is that if you need basepair-resolution pre-rendered 
graphics (which is how JBrowse handles wiggle tracks) on a gigabase 
genome, you're going to need gigabytes of storage for each track...

best wishes
Ian


Andrew Shinohara wrote:
> Hello,
>      I am generating a wiggle track for the human genome using 
> wig-to-json.pl <http://wig-to-json.pl>.  I am finding that for 1 wiggle 
> track for the human genome, it is producing about 10GB of images.  I was 
> wondering if there is any way to reduce the number/size of images 
> generated for each track?  Is it possible to give a minimum and maximum 
> zoom level so that less images are generated or something along those lines?
> 
> Thanks,
> Andrew
> 
> 
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[Gmod-ajax] Wiggle Tracks in JBrowse

[Andrew S. <ac...@ge...>]

Hello,
     I am generating a wiggle track for the human genome using
wig-to-json.pl.  I am finding that for 1 wiggle track for the human genome,
it is producing about 10GB of images.  I was wondering if there is any way
to reduce the number/size of images generated for each track?  Is it
possible to give a minimum and maximum zoom level so that less images are
generated or something along those lines?

Thanks,
Andrew

[Gmod-ajax] data format for jbrowse nclist

[James C. <ca...@gm...>]

Hi,

I really like using jbrowse, but one thing I don't like is having to
use bioperl to produce the JSON structures.  Would you consider
publishing a brief spec of the JSON expected by jbrowse so that I can
consider publishing my own JSON nested lists?

One reason I want to do this is I have some data already in JSON style
format (using mongodb) and I would rather not go SON -> GFF3 ->
bioperl -> JSON.  If you're interested, here is some (very) rough code
doing a proof of principle here:
http://github.com/jamescasbon/mongo-nclist

thanks,
James

Re: [Gmod-ajax] using multiple sources

[Adam W. <aw...@sg...>]

On 28 May 2010, at 19:13, Mitch Skinner wrote:

> On 05/28/2010 09:30 AM, Adam Witney wrote:
>> Although I now cannot seem to get the name searching to work. I have run
>> bin/generate-names.pl --dir genome1
>> 
>> and the genome1/names does contain the *.json files. I did notice that when i reload the page I get an error in the apache logs:
>> 
>> "File does not exist: /usr/local/apache2/htdocs/jbrowse/data"
>> 
>> and this in firebug:
>> 
>> "Error: Unable to load data/names/root.json status:404"
>> 
>> so it must still be looking for the "data" directory at some point. Do i have to change any other settings to use a non-default data directory?
>>   
> 
> Right, I forgot about this part.  There is a setting (the "dataRoot" option to the Browser constructor), but looking at it just now, it won't quite work in the setup that we've been discussing (it was originally aimed at a slightly different setup; it's used by the TWiki plugin).
> 
> So, right now you've got two options:
> 
> 1. have separate JBrowse directories will both code and data, or
> 2. wait a few days or a week for us to fix up the dataRoot setting to be more flexible.
> 
> If you choose option 1, and if you originally got JBrowse using git, then you can save some disk space by using "git clone".  For example, if you originally did a "git clone" to create a "jbrowse" directory, you can clone from there to a new directory, and the clone will save some disk space (by using hard-linking).
> 
> $ git clone jbrowse genome1
> $ git clone jbrowse genome2
> 
> will give you new "genome1" and "genome2" directories that don't use much extra disk space.
> 
> Sorry about that,
> Mitch

ok thanks for the tips Mitch, I will try those options

thanks

adam

Re: [Gmod-ajax] Tiling Array data and Gene report Page

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

On 5/28/2010 1:51 PM, Swapnil Nagar wrote:
> Can I generate the gene report page (as I can do it on Gbrowse 1 + )?
>    

Currently, all JBrowse can do is either 1) the little popup you get when 
you click on a feature, or 2) link to a page provided by something else.

So if you have a GBrowse instance going, then you can use JBrowse to 
link to the GBrowse gene page, so that the GBrowse gene page opens when 
you click on a gene.  You can specify that link using the "urlTemplate" 
setting in the config file (with bin/biodb-to-json.pl), or using the 
--urltemplate parameter to bin/flatfile-to-json.pl.

JBrowse by itself doesn't currently generate anything like the GBrowse 
gene pages, though.

> Second issue is with the Tiling array data, Is there is any way to represent tiling array data or in other words signal strength.
>    

If you can get the data into the wiggle format:
http://genome.ucsc.edu/goldenPath/help/wiggle.html

or the bedGraph format:
http://genome.ucsc.edu/goldenPath/help/bedgraph.html

then you can display the data in JBrowse, by running the 
bin/wig-to-json.pl program on your wiggle/bedGraph file.

Hope this helps,
Mitch

[Gmod-ajax] Tiling Array data and Gene report Page

[Swapnil N. <zea...@k-...>]

Hi,

I am working on the JBROWSE 

Can I generate the gene report page (as I can do it on Gbrowse 1 + )?

Second issue is with the Tiling array data, Is there is any way to represent tiling array data or in other words signal strength.

If there is, can I have the JSON file for that.

Regards,

Swapnil Nagar

Re: [Gmod-ajax] using multiple sources

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

On 05/28/2010 09:30 AM, Adam Witney wrote:
> Although I now cannot seem to get the name searching to work. I have run
> bin/generate-names.pl --dir genome1
>
> and the genome1/names does contain the *.json files. I did notice that when i reload the page I get an error in the apache logs:
>
> "File does not exist: /usr/local/apache2/htdocs/jbrowse/data"
>
> and this in firebug:
>
> "Error: Unable to load data/names/root.json status:404"
>
> so it must still be looking for the "data" directory at some point. Do i have to change any other settings to use a non-default data directory?
>    

Right, I forgot about this part.  There is a setting (the "dataRoot" 
option to the Browser constructor), but looking at it just now, it won't 
quite work in the setup that we've been discussing (it was originally 
aimed at a slightly different setup; it's used by the TWiki plugin).

So, right now you've got two options:

1. have separate JBrowse directories will both code and data, or
2. wait a few days or a week for us to fix up the dataRoot setting to be 
more flexible.

If you choose option 1, and if you originally got JBrowse using git, 
then you can save some disk space by using "git clone".  For example, if 
you originally did a "git clone" to create a "jbrowse" directory, you 
can clone from there to a new directory, and the clone will save some 
disk space (by using hard-linking).

$ git clone jbrowse genome1
$ git clone jbrowse genome2

will give you new "genome1" and "genome2" directories that don't use 
much extra disk space.

Sorry about that,
Mitch

Re: [Gmod-ajax] using multiple sources

[Adam W. <aw...@sg...>]

Hi Mitch,

thanks for your reply. I have multiple bacterial species and i wanted to have a new "view" for each ie each with their own list of tracks on the left hand side. This approach you suggested seems to have done the trick precisely:

> $ bin/prepare-refseqs.pl --conf config1.js --refs chr1,chr2,chr3 --out genome1-data
> $ bin/biodb-to-json.pl --conf config1.js --out genome1-data
> $ cp index.html genome1.html
> 
> and edit genome1.html so that those two lines above look like this:
> 
> <script type="text/javascript" src="genome1-data/refSeqs.js"></script>
> <script type="text/javascript" src="genome1-data/trackInfo.js"></script>

Although I now cannot seem to get the name searching to work. I have run

bin/generate-names.pl --dir genome1

and the genome1/names does contain the *.json files. I did notice that when i reload the page I get an error in the apache logs:

"File does not exist: /usr/local/apache2/htdocs/jbrowse/data"

and this in firebug:

"Error: Unable to load data/names/root.json status:404"

so it must still be looking for the "data" directory at some point. Do i have to change any other settings to use a non-default data directory?

thanks

adam

Re: [Gmod-ajax] using multiple sources

[Brenton G. <brg...@gm...>]

We have very successfully used the method Mitch mentioned of downloading/installing a separate JBrowse instance to do this for several different species (human, mouse, fly, etc.) and simply give the JBrowse directories different names (JBrowse/Human, JBrowse/Mouse, etc.) and it works great.  I agree, with Mitch that the space used up by JBrowse code is minimal with respect to the genome data.   

Brent


On May 28, 2010, at 11:27 AM, Mitch Skinner wrote:

> On 05/28/2010 07:36 AM, Adam Witney wrote:
>> Is it possible to use multiple source genomes from a single jbrowse installation?
>> 
>> I have setup a config file for each genome and can run
>> 
>> bin/biodb-to-json.pl --conf config1.js --ref genome1
>> bin/biodb-to-json.pl --conf config2.js --ref genome2
>> 
>> ok. But I can't seem to be able the second one up in the browser. Is there a specific way I should approach this? I couldn't see anything on the wiki about this
>> 
> 
> Aside: If you have multiple data sources that all describe the same 
> genome (say, a chado database, and a GFF file, and a wiggle file, all of 
> which are about the same set of reference sequences) then you can 
> certainly put them into the same JBrowse instance, like you were trying 
> to do.
> 
> It doesn't sound like that applies to you, but it's an FAQ, so I thought 
> I'd mention it.
> 
> One assumption that JBrowse makes is that each reference sequence has a 
> unique name, so if your two genomes both have, say, a "chr1" refseq, 
> then there will be confusion.   So, if each genome has multiple refseqs 
> (i.e., multiple chromosomes), then usually you want to have one genome 
> per JBrowse "instance"; an instance is one JBrowse "data" directory 
> containing the JSON files generated by biodb-to-json.pl and the other 
> JBrowse scripts.
> 
> As usual, the best thing you can do at the moment comes down to what 
> you're trying to accomplish.
> 
> If you make sure that each of the reference sequences has a unique name 
> (say, if you have multiple species that each only have one reference 
> sequence, like viruses) then you can have all your genomes in one 
> JBrowse instance.  All you have to do is make sure that run 
> bin/prepare-refseqs.pl gets run for all of the ref seqs.
> 
> Specifically, start out by doing
> 
> $ bin/prepare-refseqs.pl --conf config1.js --refs genome1
> $ bin/prepare-refseqs.pl --conf config2.js --refs genome2
> 
> and then do the bin/biodb-to-json.pl commands you were doing (you should 
> be able to leave the "--refs" argument off of the biodb-to-json.pl 
> commands, if you only have one ref per genome).
> 
> 
> On the other hand, if you're working with species with multiple 
> chromosomes, one simple thing you can do is have a whole separate 
> JBrowse download for each genome.  It takes up a little more space, but 
> the space is usually small relative to the size of the genome data.
> 
> If you have lots of different genomes and you're concerned about the 
> space taken up by having separate sets of the JBrowse code, then one 
> thing you can do is have a separate "data" directory for each genome, 
> but sharing the same JBrowse code.  Then you'd have to copy the 
> index.html file and edit these two lines:
> 
> <script type="text/javascript" src="data/refSeqs.js"></script>
> <script type="text/javascript" src="data/trackInfo.js"></script>
> 
> to refer to the specific data directories.
> 
> Specifically, I mean doing something like this:
> 
> $ bin/prepare-refseqs.pl --conf config1.js --refs chr1,chr2,chr3 --out 
> genome1-data
> $ bin/biodb-to-json.pl --conf config1.js --out genome1-data
> $ cp index.html genome1.html
> 
> and edit genome1.html so that those two lines above look like this:
> 
> <script type="text/javascript" src="genome1-data/refSeqs.js"></script>
> <script type="text/javascript" src="genome1-data/trackInfo.js"></script>
> 
> And then you'd do the same thing for genome2, with a new genome2-data 
> directory and a new genome2.html file.
> 
> Then you could link to each of those html files separately for each genome.
> 
> Comparing two genomes against each other on the same screen in a 
> synteny-style view is something we're keen to do in the JBrowse renewal, 
> but it's not currently implemented.
> 
> Does that get you where you want to go?
> 
> Mitch
> 
> ------------------------------------------------------------------------------
> 
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] using multiple sources

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

On 05/28/2010 07:36 AM, Adam Witney wrote:
> Is it possible to use multiple source genomes from a single jbrowse installation?
>
> I have setup a config file for each genome and can run
>
> bin/biodb-to-json.pl --conf config1.js --ref genome1
> bin/biodb-to-json.pl --conf config2.js --ref genome2
>
> ok. But I can't seem to be able the second one up in the browser. Is there a specific way I should approach this? I couldn't see anything on the wiki about this
>    

Aside: If you have multiple data sources that all describe the same 
genome (say, a chado database, and a GFF file, and a wiggle file, all of 
which are about the same set of reference sequences) then you can 
certainly put them into the same JBrowse instance, like you were trying 
to do.

It doesn't sound like that applies to you, but it's an FAQ, so I thought 
I'd mention it.

One assumption that JBrowse makes is that each reference sequence has a 
unique name, so if your two genomes both have, say, a "chr1" refseq, 
then there will be confusion.   So, if each genome has multiple refseqs 
(i.e., multiple chromosomes), then usually you want to have one genome 
per JBrowse "instance"; an instance is one JBrowse "data" directory 
containing the JSON files generated by biodb-to-json.pl and the other 
JBrowse scripts.

As usual, the best thing you can do at the moment comes down to what 
you're trying to accomplish.

If you make sure that each of the reference sequences has a unique name 
(say, if you have multiple species that each only have one reference 
sequence, like viruses) then you can have all your genomes in one 
JBrowse instance.  All you have to do is make sure that run 
bin/prepare-refseqs.pl gets run for all of the ref seqs.

Specifically, start out by doing

$ bin/prepare-refseqs.pl --conf config1.js --refs genome1
$ bin/prepare-refseqs.pl --conf config2.js --refs genome2

and then do the bin/biodb-to-json.pl commands you were doing (you should 
be able to leave the "--refs" argument off of the biodb-to-json.pl 
commands, if you only have one ref per genome).


On the other hand, if you're working with species with multiple 
chromosomes, one simple thing you can do is have a whole separate 
JBrowse download for each genome.  It takes up a little more space, but 
the space is usually small relative to the size of the genome data.

If you have lots of different genomes and you're concerned about the 
space taken up by having separate sets of the JBrowse code, then one 
thing you can do is have a separate "data" directory for each genome, 
but sharing the same JBrowse code.  Then you'd have to copy the 
index.html file and edit these two lines:

<script type="text/javascript" src="data/refSeqs.js"></script>
<script type="text/javascript" src="data/trackInfo.js"></script>

to refer to the specific data directories.

Specifically, I mean doing something like this:

$ bin/prepare-refseqs.pl --conf config1.js --refs chr1,chr2,chr3 --out 
genome1-data
$ bin/biodb-to-json.pl --conf config1.js --out genome1-data
$ cp index.html genome1.html

and edit genome1.html so that those two lines above look like this:

<script type="text/javascript" src="genome1-data/refSeqs.js"></script>
<script type="text/javascript" src="genome1-data/trackInfo.js"></script>

And then you'd do the same thing for genome2, with a new genome2-data 
directory and a new genome2.html file.

Then you could link to each of those html files separately for each genome.

Comparing two genomes against each other on the same screen in a 
synteny-style view is something we're keen to do in the JBrowse renewal, 
but it's not currently implemented.

Does that get you where you want to go?

Mitch

[Gmod-ajax] using multiple sources

[Adam W. <aw...@sg...>]

Hi,

Is it possible to use multiple source genomes from a single jbrowse installation?

I have setup a config file for each genome and can run 

bin/biodb-to-json.pl --conf config1.js --ref genome1
bin/biodb-to-json.pl --conf config2.js --ref genome2

ok. But I can't seem to be able the second one up in the browser. Is there a specific way I should approach this? I couldn't see anything on the wiki about this

thanks for any help

adam

Re: [Gmod-ajax] sam and bam on lazyfeatures

[Ian H. <ih...@be...>]

Hi James,

There is a (very preliminary) Dmel BAM test here:

http://jbrowse.org/test/lazyfeatures/


Of course you can also check out that branch!

Ian


James Casbon wrote:
> I was excited to see sam files mentioned in lazyfeatures ...
> http://github.com/jbrowse/jbrowse/blob/lazyfeatures/bin/flatfile-to-json.pl
> 
> Is there a demo or is it worth checking out this branch and trying it myself?
> 
> cheers,
> James
> 
> ------------------------------------------------------------------------------
> 
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
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[Gmod-ajax] sam and bam on lazyfeatures

[James C. <ca...@gm...>]

I was excited to see sam files mentioned in lazyfeatures ...
http://github.com/jbrowse/jbrowse/blob/lazyfeatures/bin/flatfile-to-json.pl

Is there a demo or is it worth checking out this branch and trying it myself?

cheers,
James

Re: [Gmod-ajax] JBrowse hg19 Demo - tracks very tall, can't zoom vertically?

[Andrew V. U. <and...@gm...>]

On Thu, Apr 29, 2010 at 12:04 PM, Andrew V. Uzilov
<and...@gm...> wrote:
> But ideally, it would be nice if you could drag and select a region to
> zoom in on.  The UCSC Genome Browser has that feature.  You can click
> and drag on the coordinates line, and a blue box appears that clearly
> delineates the new view that you will zoom to.  It is very, VERY
> useful.  So useful I opened a ticket requesting this on Lighthouse:
> #59

Oops, I think this feature has already been requested as tickets #42
and #21.  If so, sorry.

Andrew U.

Re: [Gmod-ajax] JBrowse hg19 Demo - tracks very tall, can't zoom vertically?

[Andrew V. U. <and...@gm...>]

Hi Ann....

I have some comments below, but I am also going to use your e-mail as
an excuse to comment on some feature requests I wanted to make.

On Thu, Apr 29, 2010 at 6:12 AM, Ann Loraine <alo...@gm...> wrote:
> I'm just now viewed at the demo in Firefox and Safari.
>
> The tracks look very tall when I viewed them in my two browsers (I'm
> on a Mac)  -- I can only see one at a time in my window. (Please see
> attached)
>
> There is a scrollbar for the track names on the left but I couldn't
> see a scrollbar on the right that would allow me to move up and down
> in the display. (Using the mouse scrollwheel allowed me to move up and
> down, however.)

I get the same behavior on Firefox 3.0.18 on CentOS 5 for both dmel
and hg demos -- no scroll bar for tracks themselves, but can scroll
with mouse wheel.  Opera 10.10 on same machine puts the scroll bar for
track names in the wrong place -- all the way at the right, instead of
between track label panel and track panel.

The bigger issue that you are touching on is that there ideally should
be some way to control track heights so they don't blow up like this.
I opened a ticket (#58) on the Lighthouse request/bug tracker for
JBrowse:

http://jbrowse.lighthouseapp.com/

that is basically to cap the track height so they don't blow up like that.

A ticket related to this are #57, which is to give more control over
how tracks are displayed (like their height).

> Also, how do I focus zooming? For instance, if I want to zoom in on a
> region, do I first click that region and then click the zoom icon, or
> should I instead center the display and then click the zoom icon?

You can double-click on a space in the coordinates line and you will
get zoomed in on that specific location.

But ideally, it would be nice if you could drag and select a region to
zoom in on.  The UCSC Genome Browser has that feature.  You can click
and drag on the coordinates line, and a blue box appears that clearly
delineates the new view that you will zoom to.  It is very, VERY
useful.  So useful I opened a ticket requesting this on Lighthouse:
#59

Cheers,
Andrew U.

Re: [Gmod-ajax] JBrowse hg19 Demo

[Andrew S. <ac...@ge...>]

Mitch and Ian,
     Thank you very much for the help!  I am now up and running after
switching to that commit and generating my own JSON from the BED files
that UCSC provides.

Thanks again,
Andrew

On Wed, Apr 28, 2010 at 7:48 PM, Mitch Skinner
<mit...@be...> wrote:
> The human demo uses the "lazyfeatures" branch, but the demo hasn't been
> updated to the very latest code in that branch yet.
>
> If you want to use the json files from the human demo with the code from the
> human demo, use a slightly earlier version (commit 292aa08) of the
> lazyfeatures code.  This is how I got there with git, there may be a more
> straightforward way to do this, but this is how I currently think of it:
> (this is what I did after the "git clone")
> ===============
> $ git branch
> * master
> $ git branch --track lazyfeatures origin/lazyfeatures
> Branch lazyfeatures set up to track remote branch
> refs/remotes/origin/lazyfeatures.
> $ git branch
>   lazyfeatures
> * master
> $ git checkout lazyfeatures
> Switched to branch 'lazyfeatures'
> $ git checkout 292aa08
> Note: moving to '292aa08' which isn't a local branch
> If you want to create a new branch from this checkout, you may do so
> (now or later) by using -b with the checkout command again. Example:
>   git checkout -b <new_branch_name>
> HEAD is now at 292aa08... actually set max_depth on all the writeJSON calls
> ===============
>
> Alternatively, you could download from here:
> http://github.com/jbrowse/jbrowse/archives/292aa081c37525fbf655bb99b60e466938b985bc
>
> Generally speaking, the demos aren't always using the very latest code
> because I'm often debugging the very latest code and the demos are meant to
> be a little more stable.  So I usually expect that people will want to
> generate their own json files.  If you want to do that, I've attached a list
> of the commands I used to generate the human demo.  It's not complete; it's
> just what I still have in my shell command history.  But hopefully it gives
> you a sense of how to use flatfile-to-json.pl.
>
> The attached list of commands uses BED files that I downloaded from the UCSC
> table browser as input.  Sometime soon, I'll implement a more convenient way
> of setting up a JBrowse instance from UCSC data, but currently the best
> thing to do is use BED files.
>
> Also, (with the current code) the larger tracks often work better if they're
> split up by chromosome, e.g. (using bash):
>
> ===============
> pushd ~/data/ucsc/hg19-bed
> for x in `seq 1 22` X Y; do grep "^chr$x"$'\t' SplicedESTs.bed >
> SplicedESTs-chr$x.bed; done
> popd
> for x in `seq 22 -1 1` X Y; do bin/flatfile-to-json.pl --bed
> ~/data/ucsc/hg19-bed/SplicedESTs-chr$x.bed --tracklabel SplicedESTs --key
> "Spliced ESTs" --cssClass generic_parent --subfeatureClasses '{"CDS":
> "match_part"}' --getSubs; done
> ===============
>
> But if you have enough RAM you may not need to do that.
>
> Hope this helps,
> Mitch
>
> On 04/28/2010 08:38 AM, Andrew Shinohara wrote:
>
> Hello,
>      I am viewing the tracks on the JBrowse demo site at
> http://jbrowse.org/ucsc/hg19/ and have a couple of questions.  What version
> of JBrowse is this using?  I have attempted to take the trackData.json files
> from the demo site and use them in the version of JBrowse that I checked out
> from github.  Neither branch (master or lazyfeatures) seems to be working.
> Specifically, when I add the "Ensembl Genes" track to the display, nothing
> is getting rendered.  Also, is there any documentation as to how you were
> able to generate all of the trackData.json files?  I know there is a set of
> perl scripts, but a more detailed tutorial (with example files) would be
> very useful.
>
> Thanks,
> Andrew Shinohara
>
> ------------------------------------------------------------------------------
>
>
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> Gmod-ajax mailing list
> Gmo...@li...
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>
>

[Gmod-ajax] JBrowse hg19 Demo - tracks very tall, can't zoom vertically?

[Ann L. <alo...@gm...>]

Hello,

I'm just now viewed at the demo in Firefox and Safari.

The tracks look very tall when I viewed them in my two browsers (I'm
on a Mac)  -- I can only see one at a time in my window. (Please see
attached)

There is a scrollbar for the track names on the left but I couldn't
see a scrollbar on the right that would allow me to move up and down
in the display. (Using the mouse scrollwheel allowed me to move up and
down, however.)

I'm wondering if this has something to do with the browser I'm
running, e.g., a Mac versus Windows issue or something like that?

Also, how do I focus zooming? For instance, if I want to zoom in on a
region, do I first click that region and then click the zoom icon, or
should I instead center the display and then click the zoom icon?

Lastly, there is a lot of data available on the site. Is there a way
to access it via DAS?

Very best wishes,

Ann Loraine

Re: [Gmod-ajax] JBrowse hg19 Demo

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

bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/ChromosomeBand.bed --tracklabel ChromosomeBand --key "Chromosome Band" --cssClass exon --getLabel --autoComplete label
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/CpGIslands.bed --tracklabel CpGIslands --key "CpG Islands" --cssClass basic --clientConfig '{"featureCss": "background-color: #0D0; height: 8px", "histCss": "background-color: #3D3"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/Gap.bed --tracklabel Gap --key "Gap" --cssClass --cssClass basic --clientConfig '{"featureCss": "background-color: #777; height: 8px", "histCss": "background-color: #777"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-CEU-daught-2878.bed --tracklabel "GenomeVariants-CEU-daught-2878" --key "GenomeVariants - CEU daught '2878" --cssClass basic --clientConfig '{"featureCss": "background-color: #66F; height: 8px", "histCss": "background-color: #88F"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/bacEndPairs.bed --tracklabel bacEndPairs --key "BAC End Pairs" --cssClass generic_parent --subfeatureClasses '{"CDS": "match_part"}' --getLabel --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/EnsemblGenes.bed --tracklabel EnsemblGenes --key "Ensembl Genes" --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead --getLabel --autoComplete label --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-CEU-mother-2892.bed --tracklabel "GenomeVariants-CEU-mother-2892" --key "GenomeVariants - CEU mother '2892" --cssClass basic --clientConfig '{"featureCss": "background-color: #AF6; height: 8px", "histCss": "background-color: #BF8"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-Venter.bed --tracklabel "GenomeVariants-Venter" --key "GenomeVariants - Venter" --cssClass basic --clientConfig '{"featureCss": "background-color: #FF00AF; height: 8px", "histCss": "background-color: #FF66CF"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-Watson.bed --tracklabel "GenomeVariants-Watson" --key "GenomeVariants - Watson" --cssClass basic --clientConfig '{"featureCss": "background-color: #1834BA; height: 8px", "histCss": "background-color: #576DD9"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-Yh1.bed --tracklabel "GenomeVariants-Yh1" --key "GenomeVariants - Yh1" --cssClass basic --clientConfig '{"featureCss": "background-color: #3D59CC; height: 8px", "histCss": "background-color: #5E79E6"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GWASCatalog.bed --tracklabel "GWASCatalog" --key "GWAS Catalog" --cssClass basic --clientConfig '{"featureCss": "background-color: #00F; height: 8px", "histCss": "background-color: #88F"}' --getLabel --autocomplete label
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/HumanmRNAs-all_mrna.bed --tracklabel all_mrna --key "Human mRNAs" --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead --getLabel --autoComplete label --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/MGCGenes.bed --tracklabel "MGCGenes" --key "MGC Genes" --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead --getLabel --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/N-SCAN.bed --tracklabel "N-SCAN" --key "N-SCAN" --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead --getLabel --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/RefSeqGenes.bed --tracklabel "RefSeqGenes" --key "RefSeq Genes" --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead --getLabel --getSubs --autocomplete label
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/STSMarkers.bed --tracklabel STSMarkers --key "STS Markers" --cssClass exon
history | grep flatfile-to-json | grep hg19-bed > ~/ff2json.txt
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/CCDS.bed --tracklabel CCDS --key "Consensus CDS" --cssClass generic_parent --subfeatureClasses '{"CDS": "generic_part_a"}' --getLabel
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/Exoniphy.bed --tracklabel Exoniphy --key "Exoniphy" --cssClass generic_parent --subfeatureClasses '{"CDS": "match_part"}' --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/CCDS.bed --tracklabel CCDS --key "Consensus CDS" --cssClass generic_parent --subfeatureClasses '{"CDS": "generic_part_a"}' --getLabel --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-CEU-father-2891.bed --tracklabel "GenomeVariants-CEU-father-2891" --key "GenomeVariants - CEU father '2891" --cssClass basic --clientConfig '{"featureCss": "background-color: #6F6; height: 8px", "histCss": "background-color: #8F8"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-Sjk.bed --tracklabel "GenomeVariants-Sjk" --key "GenomeVariants - Sjk" --cssClass basic --clientConfig '{"featureCss": "background-color: #BA9843; height: 8px", "histCss": "background-color: #D4B56A"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/InterruptedRpts.bed --tracklabel InterruptedRpts --key "Interrupted Rpts" --cssClass generic_parent --subfeatureClasses '{"CDS": "match_part"}' --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/MapContigs.bed --tracklabel MapContigs --key "Map Contigs" --cssClass exon
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/OMIMGenes.bed --tracklabel OMIMGenes --key "OMIM Genes" --cssClass feature
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/ORFeomeClones.bed --tracklabel ORFeomeClones --key "ORFeome Clones" --cssClass generic_parent --subfeatureClasses '{"CDS": "generic_part_a"}' --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/SegmentalDups.bed --tracklabel SegmentalDups --key "Segmental Dups" --cssClass feature5
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/SimpleRepeats.bed --tracklabel SimpleRepeats --key "Simple Repeats" --cssClass feature3
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-YRI-daught-9240.bed --tracklabel "GenomeVariants-YRI-daught-9240" --key "GenomeVariants - YRI daught '9240" --cssClass basic --clientConfig '{"featureCss": "background-color: #7245BB; height: 8px", "histCss": "background-color: #8F62D9"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/SplicedESTs.bed --tracklabel SplicedESTs --key "Spliced ESTs" --cssClass generic_parent --subfeatureClasses '{"CDS": "match_part"}' --getSubs

[Gmod-ajax] jbrowse at the VTech Pathosystems BIRC

[Ian H. <ih...@be...>]

Harry Yoo wrote:
> Hello Dr.Holmes and everyone,
> 
> This is Harry Yoo from VBI working on PATRIC BRC project. I and Ian met before, when he visited VBI.
> 
> I would like to let you know that recently we integrated JBrowse into our PATRIC BRC. The JBrowse integration at April Release was the first step, which displays and enable user to browse genomic features annotated by PATRIC, legacy BRCs, and RefSeq. There are still missing features such as searching by feature names. 
> 
> We will be working on to integrate JBrowser fully and would like to add more functionalities through a collaboration with your group.
> If you have a chance, please take a look at, and feel free to suggest or leave any comments. 
> 
> 
> Project Website
> http://www.patricbrc.org/portal/portal/patric/Home
> 
> 
> Genome browser is available at genome level page, for example,
> 
> Brucella abortus S19 home
> http://www.patricbrc.org/portal/portal/patric/Genome?cType=genome&cId=38055
> 
> You can click "Genome Browser" tab, or click genome browser icon on each sequence at sequence summary window.
> 
> 
> At any taxon level, in the "genome list" tab, JBrowser is accessible.
> 
> http://www.patricbrc.org/portal/portal/patric/GenomeList?cType=taxon&cId=234&dataSource=&displayMode=genome
> 
> 
> 
> Best wishes,
> Harry Yoo
> 
> 
> 

Re: [Gmod-ajax] JBrowse hg19 Demo

[Andrew S. <ac...@ge...>]

Ian,
     I have tried out the volvox tutorial and was successful, however;
I did not see any tutorial as to how your team arrived at a working
demo for Homo Sapiens.  Did you use the flatfile-to-json.pl script?
Where did you obtain the GFF file used in this script?  I tried to run
this script on a GFF file from:

http://www.compbio.ox.ac.uk/data/HUMAN_HG18/ensembl/chr1_ens_annots.gff

But it did not produce the desired output.  Any more detail as to how
you arrived at this working demo for Homo Sapiens would be very
helpful.

Thanks,
Andrew

On Wed, Apr 28, 2010 at 1:18 PM, Ian Holmes <ih...@be...> wrote:
>
> Thanks Andrew,
>
> The demo uses the lazyfeatures branch. I can't immediately see what the problem is; given that you are copying from a working demo, it seems like it might well be an httpd config or permissions issue at your end (or an incomplete copy), but it's hard to be sure.
>
> Can you try the tutorial(s)? It might be easier to start from scratch.
>
> Best wishes,
> Ian
>
> Andrew Shinohara wrote:
>>
>> Ian,
>>     Sorry I was not more explicit.  I have copied the entire directory tree from the demo site from data all the way down.  I am working on OS X with Firefox 3.6.3.  I have firebug up and I am not getting any 404 errors, so it looks like all of the Ajax requests are working fine.
>>
>> -Andrew
>>
>> On Wed, Apr 28, 2010 at 12:01 PM, Ian Holmes <ih...@be... <mailto:ih...@be...>> wrote:
>>
>>    Andrew,
>>
>>    You need to do more than just copy trackData.json, you need to
>>    actually generate the track files from data (or copy the entire
>>    directory tree, I suppose). There are two tutorials linked from
>>    jbrowse.org <http://jbrowse.org>.
>>
>>
>>    For future problem reports it could be useful to know what platform
>>    you're on (server & client web browser), and what you have typed at
>>    the command line.
>>
>>    Ian
>>
>>
>>    Andrew Shinohara wrote:
>>
>>        Hello,
>>            I am viewing the tracks on the JBrowse demo site at
>>        http://jbrowse.org/ucsc/hg19/ and have a couple of questions.
>>         What version of JBrowse is this using?  I have attempted to
>>        take the trackData.json files from the demo site and use them in
>>        the version of JBrowse that I checked out from github.  Neither
>>        branch (master or lazyfeatures) seems to be working.
>>         Specifically, when I add the "Ensembl Genes" track to the
>>        display, nothing is getting rendered.  Also, is there any
>>        documentation as to how you were able to generate all of the
>>        trackData.json files?  I know there is a set of perl scripts,
>>        but a more detailed tutorial (with example files) would be very
>>        useful.
>>
>>        Thanks,
>>        Andrew Shinohara
>>
>>
>>        ------------------------------------------------------------------------
>>
>>        ------------------------------------------------------------------------------
>>
>>
>>        ------------------------------------------------------------------------
>>
>>        _______________________________________________
>>        Gmod-ajax mailing list
>>        Gmo...@li...
>>        <mailto:Gmo...@li...>
>>        https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>

Re: [Gmod-ajax] JBrowse hg19 Demo

[Ian H. <ih...@be...>]

Thanks Andrew,

The demo uses the lazyfeatures branch. I can't immediately see what the 
problem is; given that you are copying from a working demo, it seems 
like it might well be an httpd config or permissions issue at your end 
(or an incomplete copy), but it's hard to be sure.

Can you try the tutorial(s)? It might be easier to start from scratch.

Best wishes,
Ian

Andrew Shinohara wrote:
> Ian,
>      Sorry I was not more explicit.  I have copied the entire directory 
> tree from the demo site from data all the way down.  I am working on OS 
> X with Firefox 3.6.3.  I have firebug up and I am not getting any 404 
> errors, so it looks like all of the Ajax requests are working fine.
> 
> -Andrew
> 
> On Wed, Apr 28, 2010 at 12:01 PM, Ian Holmes <ih...@be... 
> <mailto:ih...@be...>> wrote:
> 
>     Andrew,
> 
>     You need to do more than just copy trackData.json, you need to
>     actually generate the track files from data (or copy the entire
>     directory tree, I suppose). There are two tutorials linked from
>     jbrowse.org <http://jbrowse.org>.
> 
> 
>     For future problem reports it could be useful to know what platform
>     you're on (server & client web browser), and what you have typed at
>     the command line.
> 
>     Ian
> 
> 
>     Andrew Shinohara wrote:
> 
>         Hello,
>             I am viewing the tracks on the JBrowse demo site at
>         http://jbrowse.org/ucsc/hg19/ and have a couple of questions.
>          What version of JBrowse is this using?  I have attempted to
>         take the trackData.json files from the demo site and use them in
>         the version of JBrowse that I checked out from github.  Neither
>         branch (master or lazyfeatures) seems to be working.
>          Specifically, when I add the "Ensembl Genes" track to the
>         display, nothing is getting rendered.  Also, is there any
>         documentation as to how you were able to generate all of the
>         trackData.json files?  I know there is a set of perl scripts,
>         but a more detailed tutorial (with example files) would be very
>         useful.
> 
>         Thanks,
>         Andrew Shinohara
> 
> 
>         ------------------------------------------------------------------------
> 
>         ------------------------------------------------------------------------------
> 
> 
>         ------------------------------------------------------------------------
> 
>         _______________________________________________
>         Gmod-ajax mailing list
>         Gmo...@li...
>         <mailto:Gmo...@li...>
>         https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> 
> 

Re: [Gmod-ajax] JBrowse hg19 Demo

[Andrew S. <ac...@ge...>]

Ian,
     Sorry I was not more explicit.  I have copied the entire directory tree
from the demo site from data all the way down.  I am working on OS X with
Firefox 3.6.3.  I have firebug up and I am not getting any 404 errors, so it
looks like all of the Ajax requests are working fine.

-Andrew

On Wed, Apr 28, 2010 at 12:01 PM, Ian Holmes <ih...@be...> wrote:

> Andrew,
>
> You need to do more than just copy trackData.json, you need to actually
> generate the track files from data (or copy the entire directory tree, I
> suppose). There are two tutorials linked from jbrowse.org.
>
>
> For future problem reports it could be useful to know what platform you're
> on (server & client web browser), and what you have typed at the command
> line.
>
> Ian
>
>
> Andrew Shinohara wrote:
>
>> Hello,
>>     I am viewing the tracks on the JBrowse demo site at
>> http://jbrowse.org/ucsc/hg19/ and have a couple of questions.  What
>> version of JBrowse is this using?  I have attempted to take the
>> trackData.json files from the demo site and use them in the version of
>> JBrowse that I checked out from github.  Neither branch (master or
>> lazyfeatures) seems to be working.  Specifically, when I add the "Ensembl
>> Genes" track to the display, nothing is getting rendered.  Also, is there
>> any documentation as to how you were able to generate all of the
>> trackData.json files?  I know there is a set of perl scripts, but a more
>> detailed tutorial (with example files) would be very useful.
>>
>> Thanks,
>> Andrew Shinohara
>>
>>
>> ------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] JBrowse hg19 Demo

[Ian H. <ih...@be...>]

Andrew,

You need to do more than just copy trackData.json, you need to actually 
generate the track files from data (or copy the entire directory tree, I 
suppose). There are two tutorials linked from jbrowse.org.

For future problem reports it could be useful to know what platform 
you're on (server & client web browser), and what you have typed at the 
command line.

Ian


Andrew Shinohara wrote:
> Hello,
>      I am viewing the tracks on the JBrowse demo site at 
> http://jbrowse.org/ucsc/hg19/ and have a couple of questions.  What 
> version of JBrowse is this using?  I have attempted to take the 
> trackData.json files from the demo site and use them in the version of 
> JBrowse that I checked out from github.  Neither branch (master or 
> lazyfeatures) seems to be working.  Specifically, when I add the 
> "Ensembl Genes" track to the display, nothing is getting rendered.  
> Also, is there any documentation as to how you were able to generate all 
> of the trackData.json files?  I know there is a set of perl scripts, but 
> a more detailed tutorial (with example files) would be very useful.
> 
> Thanks,
> Andrew Shinohara
> 
> 
> ------------------------------------------------------------------------
> 
> ------------------------------------------------------------------------------
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] JBrowse hg19 Demo

[Andrew S. <ac...@ge...>]

Hello,
     I am viewing the tracks on the JBrowse demo site at
http://jbrowse.org/ucsc/hg19/ and have a couple of questions.  What version
of JBrowse is this using?  I have attempted to take the trackData.json files
from the demo site and use them in the version of JBrowse that I checked out
from github.  Neither branch (master or lazyfeatures) seems to be working.
Specifically, when I add the "Ensembl Genes" track to the display, nothing
is getting rendered.  Also, is there any documentation as to how you were
able to generate all of the trackData.json files?  I know there is a set of
perl scripts, but a more detailed tutorial (with example files) would be
very useful.

Thanks,
Andrew Shinohara

Re: [Gmod-ajax] wig-to-json.pl gives low resolution image and the values didn't correspond to the values in wig file

[CHAN, K. 1 [AG/7721] <ken...@mo...>]

Hello Mitch,
  Got it!! This is very helpful to correct my data display. Thanks a
lot!!

Regards,
Kenneth



> -----Original Message-----
> From: Mitch Skinner [mailto:mit...@be...]
> Sent: Saturday, April 24, 2010 12:13 PM
> To: CHAN, KENNETH 1 [AG/7721]
> Cc: gmo...@li...
> Subject: Re: [Gmod-ajax] wig-to-json.pl gives low resolution image and
the
> values didn't correspond to the values in wig file
> 
> Hi, I'm sorry it's taken so long for me to get back to you.
> 
> This file is in the wiggle "bed" format, which UCSC now calls the
"bedgraph"
> format.  That particular format (and not the other wiggle
> forms) is defined to use zero-based, half-open coordinates:
> http://genome.ucsc.edu/goldenPath/help/bedgraph.html
> 
> In other words, these lines in the file:
> 
> chr10   0       1       4
> chr10   2       3       5
> 
> specify that there's a value of 4 at base 0, no data at base 1, and a
value of
> 5 at base 2.  The "no data" at base 1 is what is giving you those
blank spaces.
> 
> Just add 1 to the stop positions in your data, and the blank spaces
will get
> filled in.  I attached a version of your original file where I've done
this in
> order to show exactly what I mean.
> 
> Regards,
> Mitch
> 
> CHAN, KENNETH 1 [AG/7721] wrote:
> > Thanks Mitch, I found out that the low resolution problem does not
> > happen in internet explorer (I used IE 6). But it occurs in google
> > Chrome and Firefox.
> >   The most problematic thing is not the resolution issue but the
empty
> > regions (the white vertical lines among the green bar that can be
seen
> > in the attachment) in the graph. I have manually checked the wig
file.
> > There should not be any empty regions. Would it be the problem in my
> > data or a problem in wig-to-json.pl? Again, this is the command I
used:
> >
> > ./bin/wig-to-json.pl --wig
> >
/bifx/apache/htdocs/gbrowse2/databases/te_viewer/testing/TS_76715_CG_R
> > _C overage.wig --out "event_data/TS_76715/" --key "Reads Coverage"
> > --tile "event_data/TS_76715/" --tracklabel Coverage
> >
> >
> > Regards,
> > Kenneth
> >


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