Khan, Anar | 1 Jun 01:51 2011
Picon

Feature methods in callbacks

Hi

I'm having trouble with a callback for a balloon popup. So far I have:

balloon hover = sub {
                  my $f = shift;
                  my ($note) = $f->notes;
                  # Note = truncated Notes field. Would like to show more but
                  # can't get $f->desc to work, and $description doesn't work
                  # either
                  return '<b>'.$f->display_name.'</b><br> '.$f->type.' on '.$f->ref.' '.$f->start.' to
'.$f->end.'.<br> Description '.$note.'<br> Match coordinates '.$f->target.'<br> Click for more details.';

              }

I'd like to show the full "Note" field, which I realise can be accessed using $description; but when I add
other calls to the feature object e.g. $f->target, $description no longer works. 

$f->desc returns a number which I guess is an array length - a surprise to me, because the
Bio::SeqFeature::Lite docs say desc returns a string.

$f->notes (as shown in the stanza) returns a truncated description, however I'd like to show the full caboodle.

Can anyone tell me how to extract the full note field?

I believe the feature class is Bio::SeqFeature::Lite, but a lot of the methods are undocumented and some
which purportedly work according to the GBrowse tutorial aren't listed in the Bio::SeqFeature::Lite
docs. Am I looking at the wrong class?

Thanks :)
(Continue reading)

parulk | 1 Jun 02:00 2011
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Re: Gbrowse_syn(MERCATOR/MAVID)

Thanks for a very prompt response Jason.
Sheldon could you please point to the conf. file for this data set, still
better could you provide with the data that complements this chapter?

Cheers,
Parul
> Paul -
>
> We are using examples from Colin Dewey's thesis -- see the appendix.
>  http://www.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-104.html
>
> You can download drosophila data from the AAA site
>  http://rana.lbl.gov/drosophila/alignments.html
>
> And further get to archived D.erecta and D.yakuba at Colin's site:
> http://www.biostat.wisc.edu/~cdewey/fly_CAF1/
> Which leads you to this link:
> http://www.biostat.wisc.edu/~cdewey/fly_CAF1/data/DroYak_CAF1-DroEre_CAF1.tar.gz
>
> Sheldon will hopefully have a conf file and data archived to go with the
> chapter.
>
> -jason
> On May 31, 2011, at 3:52 PM, parulk@... wrote:
>
>> For testing purpose I am using "protocol 3: Loading MERCATOR into the
>> GBrowse_syn Database" outlined in the article "UNIT 9.12 Using the
>> Generic
>> Synteny Browser (GBrowse_syn)". Post loading the alignment file I am
>> curious to test the Synteny Browser for D.erecta and D.Yakuba genomes.
(Continue reading)

Jason Stajich | 1 Jun 01:22 2011

Re: Gbrowse_syn(MERCATOR/MAVID)

Paul -

We are using examples from Colin Dewey's thesis -- see the appendix.

You can download drosophila data from the AAA site

And further get to archived D.erecta and D.yakuba at Colin's site:
Which leads you to this link:

Sheldon will hopefully have a conf file and data archived to go with the chapter.

-jason
On May 31, 2011, at 3:52 PM, parulk-7GExONQZ6ZKVc3sceRu5cw@public.gmane.org wrote:

For testing purpose I am using "protocol 3: Loading MERCATOR into the
GBrowse_syn Database" outlined in the article "UNIT 9.12 Using the Generic
Synteny Browser (GBrowse_syn)". Post loading the alignment file I am
curious to test the Synteny Browser for D.erecta and D.Yakuba genomes. Is
it possible to get gff files for aforementioned genomes as well as all the
synteny configuration files?

Thanks and regards,
Parul V. Kudtarkar


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Jiao Chen | 1 Jun 09:11 2011
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500 Internal Server error

Hello:


      I followed the steps in  the basics of the tutorial but unfortunately I  still could't see the volvox data. I'm not experienced in Apache settings and don't know why. Can you help me? I can see the "Tutorial database" in the data source.  And the sample yeast_simple  is shown well. The error is like: 

Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator, webmaster <at> localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.

More information about this error may be available in the server error log.

Apache/2.2.14 (Ubuntu) Server at localhost Port 80

 
     Thanks a lot!

Jiao Chen 
 
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Scott Cain | 1 Jun 16:47 2011
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Re: 500 Internal Server error

Hello Jiao,

When you get a 500 error, there is almost always more information in
the apache error log.  Since you seem to be using Ubuntu, that log
will be in /var/log/apache2/error.log.  If the problem isn't obvious
from the error message, please post it back to the mailing list.

Scott

2011/6/1 Jiao Chen <chjiao3456 <at> gmail.com>:
> Hello:
>       I followed the steps in  the basics of the tutorial but unfortunately
> I  still could't see the volvox data. I'm not experienced in Apache settings
> and don't know why. Can you help me? I can see the "Tutorial database" in
> the data source.  And the sample yeast_simple  is shown well. The error is
> like:
>
> Internal Server Error
>
> The server encountered an internal error or misconfiguration and was unable
> to complete your request.
>
> Please contact the server administrator, webmaster <at> localhost and inform them
> of the time the error occurred, and anything you might have done that may
> have caused the error.
>
> More information about this error may be available in the server error log.
>
> ________________________________
> Apache/2.2.14 (Ubuntu) Server at localhost Port 80
>
>      Thanks a lot!
> Jiao Chen
>
> --
> 祝好!
> 陈蛟
> 东南大学生物电子学国家重点实验室,生物信息学一室
>
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Diana Gonzalez | 1 Jun 16:55 2011
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Re: 500 Internal Server error

Hello Jiao,
You have to check that the apache user is the owner of the volvox database. You can find the apache username in /etc/apache/ennvars, usually is www-data.

greetings,
Diana




2011/6/1 Jiao Chen <chjiao3456-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
Hello:

      I followed the steps in  the basics of the tutorial but unfortunately I  still could't see the volvox data. I'm not experienced in Apache settings and don't know why. Can you help me? I can see the "Tutorial database" in the data source.  And the sample yeast_simple  is shown well. The error is like: 

Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator, webmaster <at> localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.

More information about this error may be available in the server error log.

Apache/2.2.14 (Ubuntu) Server at localhost Port 80

 
     Thanks a lot!

Jiao Chen 
 
--
祝好!

陈蛟

东南大学生物电子学国家重点实验室,生物信息学一室


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Vipin TS | 1 Jun 19:44 2011
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Re: Redirecting a gbrowse site to a gbrowse2 site


Hi Vipin,

I know exactly enough about mod_rewrite to do the things I need to do
(probably a little less, actually :-) and what you're describing isn't
one of them.  Have you tried turning on logging for mod_rewrite to see
if there is an obvious reason for it's failure?

Scott



Hi Scott,

I am completely agreeing on your statements and my objective is to invoke the default
Gbrowse instance via the base URL (for ex: http://gbrowse2.fml.tuebingen.mpg.de/).
In my understanding I believe that I don't need to use mod_rewrite functionality, instead I tried
with RewriteRule in apache configuration.

Here is my test instance's apache configuration:

<VirtualHost  127.0.0.1>
    DocumentRoot /home/kit/gb/www
    <Directory /home/kit/gb/www>
        Options Indexes FollowSymLinks MultiViews
        AllowOverride None
        Order allow,deny
        allow from all
        RewriteEngine On
        RewriteRule ^$ /cgi-bin/gbrowse
    </Directory>

    ScriptAlias /cgi-bin/ /home/kit/gb/cgi-bin/
    <Directory "/home/kit/gb/cgi-bin/">
        AllowOverride None
        Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
        Order allow,deny
        Allow from all
    </Directory>
</VirtualHost>

In my Gbrowse.conf file I defined the default instance as yeast genome browser. In theory with this configuration when I invoke the http://localhost/ page through a browser
it should point to http://localhost/cgi-bin/gbrowse/yeast page but I can see that the browser is pointing to http://localhost/yeat/ which in-turn an internal error message.

Could you please let me know if I am doing anything wrong or how can I get it work in a nice way.

Thanks in advance, Vipin
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Lincoln Stein | 1 Jun 23:16 2011
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GBrowse 2.34 available

Hi,


I've released version 2.34 of GBrowse to both Sourceforge and CPAN. Here is the change log.

2.34
   * Fix broken https:// links in karyotype summary table; patch courtesy Dan Bolser
   * Fix behavior of "q" parameter to match the documented behavior.
   * Fix RemoteSet to avoid failures due to nonexistence of download directory.
   * Fix bug that allowed unauthorized users to view restricted tracks under
     following circumstances: FastCGI activated, track configuration changed, server
     not restarted.
   * Added an LDAP authentication plugin (LDAPAuthenticate).
   * Clean up appearance of favorite stars and checkboxes to deconfuse users.

The last change addresses recent concerns about the confusing track selection UI.

Lincoln

On Tue, May 31, 2011 at 4:12 PM, Lincoln Stein <lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Hi David,

It is committed to the git "master" branch. Could you check it out and see if it meets your needs?

Lincoln


On Tue, May 31, 2011 at 3:42 PM, David M. Goodstein <dmgoodstein-/3juihCSby0@public.gmane.org> wrote:

On May 18, 2011, at 7:41 AM, Lincoln Stein wrote:

Your recommendations are noted. I got rid of the checkboxes after showing various local OICR users the design in which the checkboxes and stars were side-by-side, as well as the one in which the checkboxes were to the left and the stars to the right. They were confused by the former design and thought the latter design was "ugly."

How about I put a light gray checkmark image to the left of the track name. When people click on it it turns dark?

Lincoln, is that patch imminent?

thx,

-David



Lincoln

On Wed, May 18, 2011 at 9:45 AM, Barris, Wes <Wes.Barris-S9oR8evKblOZMa5wjJbNzQC/G2K4zDHf@public.gmane.org> wrote:
Scott Cain wrote on 2011-05-17:

> Hi David,
>
> Issue one sure sounds like a bug.
>
> I was worried about issue two--the problem we were trying to solve was
> that having both the checkbox and the star resulted in a confusing
> user interface as well.  I'm still not sure what to do about.

For what it's worth, I was going to ask about the same thing at some point.
Without a visible checkbox, an unsuspecting user does not know where to click
to enable that track.  I second David's suggestion about making the checkbox
visible and possibly moving the star to the end of the track name.


> Scott
>
>
> On Tue, May 17, 2011 at 3:13 PM, David M. Goodstein
> <dmgoodstein-/3juihCSby0@public.gmane.org> wrote:
>> There seem to be a couple of  javascript/CSS issues on the Select
>> Tracks panel in v2.32 of Gbrowse: 1) for some categories, "All on" and
>> "All off" have no effect.  For the conf file brachy.conf (attached
>> here), the track category General behaves as expected:  clicking All On
>> activates a checkmark next to all the General tracks, All off clears
>> it.  However, for categories Transcripts and Analysis, All on and All
>> off have no effect in terms of checkmarks or activating tracks, they
>> are also not mutually exclusive (you can select both All on and All off
>> simultaneously. Firebug shows a "track_title is null in var ancestor =
>> track_titile.ancestors.find( " error in buttons. js, line 39, when the
>> troublesome categories are clicked. 2 ) there is no checkbox glyph next
>> to any of the tracks.  This leads the vast majority of users to try to
>> select a track by clicking on the "Favorite" star, which of course does
>> not activate a track.  It's very unintuitive that, to activate a track,
>> one should click "near" a track name but make sure not to check the
>> star!  Is there a way to get that checkbox back in the CSS? thanks,
>> -David
>>
>>
>>
>>
>>
>> David M. Goodstein, Ph.D.
>> Joint Genome Institute / Lawrence Berkeley National Lab Center for
>> Integrative Genomics / UCBerkeley http://www.phytozome.net
>>
>>
>>
>> -------------------------------------------------------------------- -
>> - -------- Achieve unprecedented app performance and reliability What
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101 College St., Suite 800
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416 673-8514
Assistant: Renata Musa <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>

David M. Goodstein, Ph.D.
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Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley




--
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Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa-O2sQSXo6EZM@public.gmane.orgca>



--
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Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>
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Fahlgren, Noah | 2 Jun 02:24 2011

Semantic zooming problems

I was recently running GBrowse 2.25 and upgraded to 2.33 (and today 2.34). As soon as I did GBrowse crashed on
me. I think I managed to isolate the problem to one (or more) instances of semantic zooming I had set up.

Below 1.4 Mbps I display gene features with generic glyphs:

[GENES]
feature         = gene pseudogene transposable_element_gene
database        = annotations
glyph           = generic
key             = Genes
height          = 6
fgcolor         = \&colorGenesByType
bgcolor         = \&colorGenesByType
strand_arrow    = 1
description     = 1
label           = 1
label density   = 25
balloon hover   = \&geneBalloon
link            = AUTO
category        = Genes

Above I display a BigWig density track:

[GENES:1400000]
database        = GeneDensity
feature         = summary
glyph           = wiggle_xyplot
height          = 25
min_score       = 0
max_score       = 1
bgcolor         = darkblue
link            = 0

Here is the BigWig database config:

[GeneDensity:database]
db_adaptor    = Bio::DB::BigWig
db_args       = -bigwig /data/www/GB2/html/databases/BigWig/gene_density_w100k_s1k.bw
        -fasta /data/www/GB2/html/databases/BigWig/A.thaliana.tair9.chr.fasta

I only get one error in the Apache log file:
Can't call method "code_setting" on an undefined value at
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 214.

I verified that I can display the BigWig feature on it's own and other BigWig-only tracks are showing up fine.

Here is what I have installed:
GBrowse 2.34
Bio::DB::BigFile 1.06 (recompiled the Kent src directory also)
Bio::Graphics 2.24
BioPerl-live 1.6.901

Thanks,
Noah Fahlgren
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Tirza Doniger | 2 Jun 08:47 2011
Picon
Picon

Re: wiggle_xyplot

Hi Tim,

Thanks for the reply. I will try playing around with the bam2wig.pl settings.

 I am still having weird 'histogram' issues even with the BigWig files. I know these Bigwig files are ok -- because
I can plot them both - separately-- not using histogram ----what can be causing this weird behavior. I also tried changing all the values from 0 to .001 -- but I got the came result-- is there some type of default setting causing this behavior. (see attached files)

Thanks,

Tirza

hybrid track (no graph_type):
[tbrucei_coverage_hybrid]
feature       = tbrucei_coverage
glyph         = hybrid_plot
min_score     = -10
max_score     = 10
height        = 70
scale         = left
clip         = 1
bicolor_pivot= zero
pos_color    = blue
neg_color    = red
label         = 0
key           = Read count (log2)

with histogram indicated:
[tbrucei_coverage_hybrid]
feature       = tbrucei_coverage
glyph         = hybrid_plot
graph_type    = histogram
min_score     = -10
max_score     = 10
height        = 70
scale         = left
clip         = 1
bicolor_pivot= zero
pos_color    = blue
neg_color    = red
label         = 0
key           = Read count (log2)


On Tue, May 31, 2011 at 10:53 AM, Tirza Doniger <tirza-5sqebsHTntQYXF1SDrpTllhkA7yGAbr7@public.gmane.org> wrote:
Hi Tim,

Thanks for all your patience!!! The problem seems to be the S P A C I N G in the conf file. I removed all the extraneous spacing and walla.....the data appeared...............................

One other question -- if you look at the track coming from the bam file (data in blue) and the data from the bigwig file in red- it looks like the reads - moved slightly to the right--- do you understand why this would happen?

I really appreciate your help with this.....hope....the rest goes smoothly.....

Thanks,
Tirza




On Tue, May 31, 2011 at 7:23 AM, Timothy Parnell <Timothy.Parnell-xpE/FmUf0Yn2fBVCVOL8/A@public.gmane.org> wrote:
Hi Tirza,
Sorry you're having such problems with this. The content of your stanza looks right. However, I noticed that you have spaces at the beginning of some of your lines; not sure if this is email formatting issues or not, but beginning whitespace isn't tolerated and the glyph will fail to render.

Otherwise, I might suspect the way you're generating your bigWig files. Here is a sample command for my bam2wig.pl script to get identical output as with using wiggle_xyplot glyph with the bam database:
bam2wig.pl --coverage --bw --in <filename>

Here is what I think you want with coverage, fixStep format, forward strand only, allowing splices, and converted to log2:
bam2wig.pl --position span --inter --strand f --splice --log 2 --bw —in <filename>

To check what's in the bigWig file and manually inspect a region that you're simultaneously viewing in GBrowse, you can use Kent's bigWigToWig utility:
bigWigToWig -chrom=<chr> -start=<start> -end=<end> in.bw out.wig

Hope this helps,
Date: Mon, 30 May 2011 04:05:43 -0600
To: Timothy Parnell <timothy.parnell-xpE/FmUf0Yn2fBVCVOL8/A@public.gmane.org<mailto:timothy.parnell-xpE/FmUf0YnGTqeKRyC1WQ@public.gmane.orgdu>>, "gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org>" <gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org>>
Subject: Re: [Gmod-gbrowse] wiggle_xyplot

Hi Tim,

Thanks for your reply. I am still having trouble. I think it would be unlikely that it would be reads from both strands as -- there are only reads from one strand.
I tried as you suggested just trying to display a wiggle_xyplot from one of the bigwig files:

[BigWig:database]
db_adaptor    =  Bio::DB::BigWig
db_args       = -bigwig  /private/software/var/lib/gbrowse2/databases/tbrucei/DS2_vs_chrom6_sorted_r.bw
                    -fasta  /private/software/var/lib/gbrowse2/databases/tbruceisam/Tb927_06_v4.fa

[BigWigIntervals]
 feature  = summary
 database = BigWig
 glyph    = wiggle_xyplot
 graph_type=histogram
 min_score = 0
 max_score = 20
 key       = wiggle plot log2
scale =left
height         = 50
fgcolor        = black
category       = BigWig
label          = 0 # Labels on wiggle tracks are redundant.
scale          = left
image_padding = 50

--------------------------------------------------
This produces a blank track on the viewer. I tried with the bigwig from both strands. No errors in the apache erro log.
I'm not sure what I am missing or doing wrong here? I have tried playing with almost all the configurations -- but have not had success?

Any ideas?

Thanks,
Tirza

On Mon, May 30, 2011 at 6:18 AM, Timothy Parnell <Timothy.Parnell <at> hci.utah.edu<mailto:Timothy.Parnell-xpE/FmUf0Yn2fBVCVOL8/A@public.gmane.org>> wrote:
Hi Tirza,

It looks like in your hybrid_plot glyph the two strands are being drawn on top of each other. You need to convert the reverse strand to all negative values. You can do this two ways: The hard way is to generate a new wig file (either from the bam file again or form the bigWig file you already created using bigWigToWig) and then prepend a '-' sign to the values using your favorite text editor, line editor, or perl one-liner. Then regenerate the bigWig file from your new negative wig file. Or the easy way is to set the 'flip_sign' option to true in the hybrid_plot conf stanza; this will automatically treat wigfileB data as negative. In either case, be sure to set the min_score in the conf stanza to a negative value.

The GFF3 file that points to the pair of bigWig files you created will also need to be loaded into a SQL Bio::DB::SeqFeature::Store database and referenced in the conf, along with the feature type. You do not need to set up a separate bigWig database conf stanza if you're using the hybrid_plot glyph; it'll automatically take care of that for you.

You may also want to try a simple wiggle_xyplot or wiggle_whiskers plot with one of the bigWig files to make sure it looks right before attempting the hybrid plot. This, of course, will require a database conf stanza.

One other thing I thought about and didn't mention before – is this RNASeq with splices? In other words, did the aligner allow for splice junctions? (TopHat, for example, does). In which case,  you may want to set the --splice option in my bam2wig.pl<http://bam2wig.pl>, which will force to report coverage only over the aligned portions and not the splice. Otherwise you will see high coverage over introns as well. It's possible this is what you are seeing….

As to the colors, the colors are hard coded to orange and blue for wigfileA and wigfileB, respectively, at least according to the documentation. Evidently, the bicolor_pivot option overrides this if you have values on  both sides of the pivot point, since that is what I see.

Hope that helps,
Tim




Date: Sun, 29 May 2011 04:47:01 -0600
To: Timothy Parnell <timothy.parnell-xpE/FmUf0Yn2fBVCVOL8/A@public.gmane.org<mailto:timothy.parnell <at> hci.utah.edu><mailto:timothy.parnell-xpE/FmUf0Yn2fBVCVOL8/A@public.gmane.org<mailto:timothy.parnell <at> hci.utah.edu>>>
Cc: "gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneHXe+LvDLADg@public.gmane.orgrceforge.net><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org>>" <gmod-gbrowse-5NWGOfrQmneHXe+LvDLADg@public.gmane.orgrceforge.net<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5urNAH6kLmebB@public.gmane.org.net>>>
Subject: Re: [Gmod-gbrowse] wiggle_xyplot

Hi Tim,

Thanks for your replies and your detailed explanations. I tried to follow your directions as detailed in the link below, but I'm still having some difficulty.

1. I installed the bigWig adaptor
2. I ran bam2wig.pl<http://bam2wig.pl><http://bam2wig.pl> twice once for each strand:

/private/software/packages/biotoolbox/scripts/bam2wig.pl<http://bam2wig.pl><http://bam2wig.pl> --in /private/software/var/lib/gbrowse2/databases/tbruceisam/DS2_vs_chrom6_sorted.bam --log 2 --strand r --out DS2_vs_chrom6_sorted_r --inter  --bw --bwapp /path/2/wigToBigWig
/private/software/packages/biotoolbox/scripts/bam2wig.pl<http://bam2wig.pl><http://bam2wig.pl> --in /private/software/var/lib/gbrowse2/databases/tbruceisam/DS2_vs_chrom6_sorted.bam --log 2 --strand f --out DS2_vs_chrom6_sorted_f --inter --bw --bwapp /path/2/wigToBigWig

2. my conf file was adjusted as follows:
[tbrucei_coverage_hybrid]
#database     = tbrucei_chr6
feature       = tbrucei_coverage
glyph         = hybrid_plot
graph_type    = histogram
min_score     = 0
max_score     = 20
height        = 70
scale         = left
#clip          = 1
bicolor_pivot = zero
pos_color     = blue
neg_color     = red
label         = 0
key           = Coverage (xyplot,log2)
category      = RNA-Seq
---------------------------------------
3. gff3 file:
##gff-version 3
Tb927_06_v4     .       tbrucei_coverage        1       1618916 .       .       .       Name=tbrucei_coverage;wigfileA=/private/software/var/lib/gbrowse2/databases/tbrucei/DS2_vs_chrom6_sorted_r.bw;wigfileB=/private/software/var/lib/gbrowse2/databases/tbrucei/DS2_vs_chrom6_sorted_r.bw;fasta=/private/software/var/lib/gbrowse2/databases/tbruceisam/Tb927_06_v4.fa


4. a.do I still need to indicate a database?

#[tbrucei_chr6:database]
#db_adaptor    = Bio::DB::BigWigSet
#db_args       = -dir /private/software/var/lib/gbrowse2/databases/tbrucei
#               -feature_type summary

  b. even when there are zero reads still seeing pileup?
  c. why does color come out orange and not blue or red?

Thanks so much!!!
Tirza

===========================================================================================

I'm glad the program worked for you.

Unfortunately, what you are seeing with the wiggle adapter is actually pretty normal. The way the Bio::Graphics module grabs the data from the wib file and then selects the data points to draw on the image unfortunately leads to the skipping of some data points. When a data point has no data, it simply extends from the previously drawn data point, leading to this appearance of signal where there is not supposed to be any. If you go back to last year, you'll see some earlier posts of mine regarding this behavior.

The solution I've found is to switch completely to the bigWig adapter. In general, bigWig is much faster, more versatile, and more reliable than the wiggle adapter in Bio::Graphics. Unfortunately, it takes a little more effort to get installed.

To illustrate this point, I generated both variableStep and fixedStep (step=1 span=1) wig files representing the coverage of a published RNASeq Bam file. I also converted these same wig files to bigWig files. I then took a screen shot of all five tracks (two wig, two bigWig, one Bam). All tracks used the wiggle_xyplot glyph and histogram graph_type. I think the differences are pretty evident.

As to your second question, take a look at the documentation for the Hybrid Plot glyph. It accepts two wig (or bigWig) files. I've posted more detailed info here
http://generic-model-organism-system-database.450254.n5.nabble.com/help-with-hybrid-plot-glyph-tp4272497p4276474.html

Tim


Date: Thu, 26 May 2011 05:45:25 -0600
To: Timothy Parnell <timothy.parnell-xpE/FmUf0Yn2fBVCVOL8/A@public.gmane.org<mailto:timothy.parnell <at> hci.utah.edu><mailto:timothy.parnell-xpE/FmUf0Yn2fBVCVOL8/A@public.gmane.org<mailto:timothy.parnell-UO+XZW7URmE@public.gmane.orgh.edu>><mailto:timothy.parnell-xpE/FmUf0Yn2fBVCVOL8/A@public.gmane.org<mailto:timothy.parnell-21b0SoolYK4@public.gmane.orgah.edu><mailto:timothy.parnell-xpE/FmUf0Yn2fBVCVOL8/A@public.gmane.org<mailto:timothy.parnell-xpE/FmUf0YnhvxM+mQhndA@public.gmane.orgedu>>>>
Cc: "gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneHXe+LvDLADg@public.gmane.orgrceforge.net><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org>><mailto:gmod-gbrowse-5NWGOfrQmneHXe+LvDLADg@public.gmane.orgrceforge.net<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5urNAH6kLmebB@public.gmane.org.net>>>" <gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org><mailto:gmod-gbrowse-5NWGOfrQmnegEbju0hdhLg@public.gmane.orgorge.net<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org>><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5urNAH6kLmebB@public.gmane.org.net><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org>>>>
Subject: Re: [Gmod-gbrowse] wiggle_xyplot

Hi Tim,

Thank you so much for your suggestions. I used the bam2wig.pl<http://bam2wig.pl><http://bam2wig.pl><http://bam2wig.pl> file as you mentioned.

I have a few questions:
1. When I tried to display the wig file on the viewer-- when there are no reads --it still displays . I have tried using the box and histogram presentation.I have attached 2 pictures of the viewer, and pasted part of the relevant section of the WIG file below. (note this from a fixed step wig file. I tried variable step as well.)

2.Using WIG, is it possible to show both strands on the same track in different colors?

Thanks so much!
Tirza

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On Wed, May 25, 2011 at 6:28 PM, Timothy Parnell <Timothy.Parnell <at> hci.utah.edu<mailto:Timothy.Parnell-xpE/FmUf0Yn2fBVCVOL8/A@public.gmane.org><mailto:Timothy.Parnell <at> hci.utah.edu<mailto:Timothy.Parnell-xpE/FmUf0Yn2fBVCVOL8/A@public.gmane.org>><mailto:Timothy.Parnell <at> hci.utah.edu<mailto:Timothy.Parnell-xpE/FmUf0Yn2fBVCVOL8/A@public.gmane.org><mailto:Timothy.Parnell <at> hci.utah.edu<mailto:Timothy.Parnell-xpE/FmUf0Yn2fBVCVOL8/A@public.gmane.org>>>> wrote:
Hi Tirza,
I assume you're talking about the coverage plot using the bam file as the source. The scale is simply a linear scale, and there currently isn't a method to transform the numbers on the fly. Instead, you'll need to precompute these values yourself.

You can generate a wig file of the sequence coverage from the bam file, and then perform the manipulation on the values in the wig file. There are several programs for calculating the coverage: the genomeCoverageBed.pl script that comes with Bio-SamTools module and the genomeCoverageBed program from the BedTools package, are two readily available solutions.

But if you want to save time, I would recommend a script that I've written (bam2wig.pl<http://bam2wig.pl><http://bam2wig.pl><http://bam2wig.pl>) that will perform the coverage calculation and convert to log scale, if you wish, as well as a number of other things. You can find the description here http://code.google.com/p/biotoolbox/wiki/Pod_bam2wig

Hope that helps,
Tim

From: Tirza Doniger <tirza-5sqebsHTntQYXF1SDrpTllhkA7yGAbr7@public.gmane.org<mailto:tirza-5sqebsHTntQYXF1SDrpTllhkA7yGAbr7@public.gmane.org><mailto:tirza-5sqebsHTntQYXF1SDrpTllhkA7yGAbr7@public.gmane.org<mailto:tirza-5sqebsHTntQYXF1SDrpTllhkA7yGAbr7@public.gmane.org>><mailto:tirza-5sqebsHTntQYXF1SDrpTllhkA7yGAbr7@public.gmane.org<mailto:tirza-5sqebsHTntQYXF1SDrpTllhkA7yGAbr7@public.gmane.org><mailto:tirza-5sqebsHTntQYXF1SDrpTllhkA7yGAbr7@public.gmane.org<mailto:tirza-5sqebsHTntQYXF1SDrpTllhkA7yGAbr7@public.gmane.org>>><mailto:tirza-5sqebsHTntQYXF1SDrpTllhkA7yGAbr7@public.gmane.org<mailto:tirza-5sqebsHTntQYXF1SDrpTllhkA7yGAbr7@public.gmane.org><mailto:tirza <at> biomodel.os.biu.ac.il<mailto:tirza-5sqebsHTntQYXF1SDrpTllhkA7yGAbr7@public.gmane.org>><mailto:tirza <at> biomodel.os.biu.ac.il<mailto:tirza-5sqebsHTntQYXF1SDrpTllhkA7yGAbr7@public.gmane.org><mailto:tirza-5sqebsHTntRFtd1xIPRryQ@public.gmane.org.biu.ac.il<mailto:tirza-5sqebsHTntQYXF1SDrpTllhkA7yGAbr7@public.gmane.org>>>>>
Date: Wed, 25 May 2011 05:03:59 -0600
To: "gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse <at> lists.sourceforge.net><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org>><mailto:gmod-gbrowse <at> lists.sourceforge.net<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmnfLDRD5uJR0wg@public.gmane.orgeforge.net>>><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org><mailto:gmod-gbrowse <at> lists.sourceforge.net<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org>><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmnfLDRD5uJR0wg@public.gmane.orgeforge.net><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org>>>>" <gmod-gbrowse <at> lists.sourceforge.net<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmnfLDRD5uJR0wg@public.gmane.orgeforge.net>><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org><mailto:gmod-gbrowse-5NWGOfrQmnfLDRD5uJR0wg@public.gmane.orgeforge.net<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org>>><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmnfLDRD5uJR0wg@public.gmane.orgeforge.net><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org>><mailto:gmod-gbrowse-5NWGOfrQmnfLDRD5uJR0wg@public.gmane.orgeforge.net<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org><mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5upmplPMkL2fr@public.gmane.orget>>>>>
Subject: [Gmod-gbrowse] wiggle_xyplot

Hi,

I have created a track representing next generation sequecing data using a bam file.. What is the default scale used? Is there a way to change the scale to a logarithmic scale- say log 2?

1.Generic Genome Browser version 2.33
2. Bio-SamTools-1.28
3. perl, v5.8.8
4. samtools-0.1.16
5. Bio::Graphics-2.21

Thanks,
Tirza
--
Tirza Doniger, Ph.D.
Bioinformatics Unit
The Mina and Everard Faculty of Life Sciences
Bar Ilan University
Phone: +972 3 531 8124
Cell: +972 52 530 8192
======================
 Life is like riding a bicycle. To keep your balance you must keep moving.
-----Albert Einstein




--
Tirza Doniger, Ph.D.
Bioinformatics Unit
The Mina and Everard Faculty of Life Sciences
Bar Ilan University
Phone: +972 3 531 8124
Cell: +972 52 530 8192
======================
 Life is like riding a bicycle. To keep your balance you must keep moving.
-----Albert Einstein




--
Tirza Doniger, Ph.D.
Bioinformatics Unit
The Mina and Everard Faculty of Life Sciences
Bar Ilan University
Phone: +972 3 531 8124
Cell: +972 52 530 8192
======================
 Life is like riding a bicycle. To keep your balance you must keep moving.
-----Albert Einstein




--
Tirza Doniger, Ph.D.
Bioinformatics Unit
The Mina and Everard Faculty of Life Sciences
Bar Ilan University
Phone: +972 3 531 8124
Cell: +972 52 530 8192
======================
 Life is like riding a bicycle. To keep your balance you must keep moving.
-----Albert Einstein




--
Tirza Doniger, Ph.D.
Bioinformatics Unit
The Mina and Everard Faculty of Life Sciences
Bar Ilan University
Phone: +972 3 531 8124
Cell: +972 52 530 8192
======================
 Life is like riding a bicycle. To keep your balance you must keep moving.
-----Albert Einstein




--
Tirza Doniger, Ph.D.
Bioinformatics Unit
The Mina and Everard Faculty of Life Sciences
Bar Ilan University
Phone: +972 3 531 8124
Cell: +972 52 530 8192
======================
 Life is like riding a bicycle. To keep your balance you must keep moving.
-----Albert Einstein

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