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Re: [Gmod-gbrowse] wiggle track won't display

From: Don Gilbert <gilbertd@cr...> - 2008-12-21 19:57

Brent,

You will want to edit both the GFF and config files to give each
track a separate "source" field to distinguish them as tracks:

wiggle.GFF:
chr1   sex       mRNA-Seq
chr1   asex      mRNA-Seq
      ^^ source   ^^ type  fields in gff

gbrowse.CONF:
[Sexual_IR_mRNA-Seq_001]
feature        = mRNA-Seq:sex   << append source

[Asexual_NIR_mRNA-Seq_001]
feature        = mRNA-Seq:asex

-- Don

Re: [Gmod-gbrowse] wiggle track won't display

From: Brenton Graveley <brgraveley@gm...> - 2008-12-21 20:32

Hi Don,

I manually changed the GFF file and uploaded them into the mysql and  
changed the config file accordingly.  However, they still all just  
show up on one track.

Below are the entries in the config file for these.  I've actually  
commented all of the specific entries out (the bottom 4) and they  
still all show up.  However, if I comment out the first one  
[track_001], none of them show up at all.

Can you see anything else that looks incorrect?

As an aside, I'd like the scale to be set on "auto" so that the height  
scales to the max in the viewing window, but it seems to scale to the  
max in the chromosome.  Is there a way to do this?

Thanks,

Brent




[track_001]
feature        = mRNA-Seq
glyph          = wiggle_xyplot
graph_type     = boxes
height         = 50
scale          = right
bgcolor        = blue
min_score      = 0
max_score      = 50
category       = mRNA-Seq
description    = mRNA-Seq from Sexual Nonirradiated
key            = Sexual_NIR-mRNA-Seq

#[Sexual_NIR_mRNA-Seq]
#feature        = mRNA-Seq:Sexual_NIR
#glyph          = wiggle_xyplot
#graph_type     = boxes
#height         = 50
#scale          = right
#bgcolor        = blue
#min_score      = 0
#max_score      = 50
#category       = mRNA-Seq
#description    = mRNA-Seq from Sexual Nonirradiated
#key            = Sexual_NIR_mRNA-Seq

#[Sexual_IR_mRNA-Seq]
#feature        = mRNA-Seq:Sexual_IR
#glyph          = wiggle_xyplot
#graph_type     = boxes
#height         = 50
#scale          = right
#bgcolor        = blue
#min_score      = 0
#max_score      = 50
#category       = mRNA-Seq
#description    = mRNA-Seq from Sexual Irradiated
#key            = Sexual_IR_mRNA-Seq

#[Asexual_NIR_mRNA-Seq]
#feature        = mRNA-Seq:Asexual_NIR
#glyph          = wiggle_xyplot
#graph_type     = boxes
#height         = 50
#scale          = right
#bgcolor        = blue
#min_score      = 0
#max_score      = 50
#category       = mRNA-Seq
#description    = mRNA-Seq from Asexual Nonirradiated
#key            = Asexual_NIR_mRNA-Seq

#[Asexual_IR_mRNA-Seq]
#feature        = mRNA-Seq:Asexual_IR
#glyph          = wiggle_xyplot
#graph_type     = boxes
#height         = 50
#scale          = right
#bgcolor        = blue
#min_score      = 0
#max_score      = 50
#category       = mRNA-Seq
#description    = mRNA-Seq from Asexual Irradiated
#key            = Asexual_IR_mRNA-Seq

On Dec 21, 2008, at 2:57 PM, Don Gilbert wrote:

>
> Brent,
>
> You will want to edit both the GFF and config files to give each
> track a separate "source" field to distinguish them as tracks:
>
> wiggle.GFF:
> chr1   sex       mRNA-Seq
> chr1   asex      mRNA-Seq
>      ^^ source   ^^ type  fields in gff
>
> gbrowse.CONF:
> [Sexual_IR_mRNA-Seq_001]
> feature        = mRNA-Seq:sex   << append source
>
> [Asexual_NIR_mRNA-Seq_001]
> feature        = mRNA-Seq:asex
>
> -- Don

Re: [Gmod-gbrowse] wiggle track won't display

From: Sheldon McKay <sheldon.mckay@gm...> - 2008-12-21 22:08

Hi Brenton,

Using the syntax in your 'track_01' config stanza, the expected
behavior is to display all features of type 'mRNA-Seq', regardless of
source.  The specific track config stanzas you commented out should
display only the specific type, identified by mRNA-Seq:sourcename.
You did not attach a copy of your new GFF but it should have the
second column populated by 'Asexual_NIR', etc.
For loading the new GFF into your database, you will either have to
remove the original GFF features or else reload the whole database
from scratch with the new GFF.

Sheldon

On Sun, Dec 21, 2008 at 3:31 PM, Brenton Graveley <brgraveley@...> wrote:
> Hi Don,
>
> I manually changed the GFF file and uploaded them into the mysql and
> changed the config file accordingly.  However, they still all just
> show up on one track.
>
> Below are the entries in the config file for these.  I've actually
> commented all of the specific entries out (the bottom 4) and they
> still all show up.  However, if I comment out the first one
> [track_001], none of them show up at all.
>
> Can you see anything else that looks incorrect?
>
> As an aside, I'd like the scale to be set on "auto" so that the height
> scales to the max in the viewing window, but it seems to scale to the
> max in the chromosome.  Is there a way to do this?
>
> Thanks,
>
> Brent
>
>
>
>
> [track_001]
> feature        = mRNA-Seq
> glyph          = wiggle_xyplot
> graph_type     = boxes
> height         = 50
> scale          = right
> bgcolor        = blue
> min_score      = 0
> max_score      = 50
> category       = mRNA-Seq
> description    = mRNA-Seq from Sexual Nonirradiated
> key            = Sexual_NIR-mRNA-Seq
>
> #[Sexual_NIR_mRNA-Seq]
> #feature        = mRNA-Seq:Sexual_NIR
> #glyph          = wiggle_xyplot
> #graph_type     = boxes
> #height         = 50
> #scale          = right
> #bgcolor        = blue
> #min_score      = 0
> #max_score      = 50
> #category       = mRNA-Seq
> #description    = mRNA-Seq from Sexual Nonirradiated
> #key            = Sexual_NIR_mRNA-Seq
>
> #[Sexual_IR_mRNA-Seq]
> #feature        = mRNA-Seq:Sexual_IR
> #glyph          = wiggle_xyplot
> #graph_type     = boxes
> #height         = 50
> #scale          = right
> #bgcolor        = blue
> #min_score      = 0
> #max_score      = 50
> #category       = mRNA-Seq
> #description    = mRNA-Seq from Sexual Irradiated
> #key            = Sexual_IR_mRNA-Seq
>
> #[Asexual_NIR_mRNA-Seq]
> #feature        = mRNA-Seq:Asexual_NIR
> #glyph          = wiggle_xyplot
> #graph_type     = boxes
> #height         = 50
> #scale          = right
> #bgcolor        = blue
> #min_score      = 0
> #max_score      = 50
> #category       = mRNA-Seq
> #description    = mRNA-Seq from Asexual Nonirradiated
> #key            = Asexual_NIR_mRNA-Seq
>
> #[Asexual_IR_mRNA-Seq]
> #feature        = mRNA-Seq:Asexual_IR
> #glyph          = wiggle_xyplot
> #graph_type     = boxes
> #height         = 50
> #scale          = right
> #bgcolor        = blue
> #min_score      = 0
> #max_score      = 50
> #category       = mRNA-Seq
> #description    = mRNA-Seq from Asexual Irradiated
> #key            = Asexual_IR_mRNA-Seq
>
> On Dec 21, 2008, at 2:57 PM, Don Gilbert wrote:
>
>>
>> Brent,
>>
>> You will want to edit both the GFF and config files to give each
>> track a separate "source" field to distinguish them as tracks:
>>
>> wiggle.GFF:
>> chr1   sex       mRNA-Seq
>> chr1   asex      mRNA-Seq
>>      ^^ source   ^^ type  fields in gff
>>
>> gbrowse.CONF:
>> [Sexual_IR_mRNA-Seq_001]
>> feature        = mRNA-Seq:sex   << append source
>>
>> [Asexual_NIR_mRNA-Seq_001]
>> feature        = mRNA-Seq:asex
>>
>> -- Don
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



-- 
Sheldon J. McKay, PhD
Research Investigator
Cold Spring Harbor Laboratory
Office: 516-367-6998
Fax: 516 367-6851
Email: mckays@...
Skype: mckays630

Re: [Gmod-gbrowse] wiggle track won't display

From: Brenton Graveley <brgraveley@gm...> - 2008-12-21 19:28

Attachments: Message as HTML

Hi,

By some "miracle" that I do not understand, I got the wiggle files to  
display.

One thing I do not understand is how to make the wiggle tracks  
separate tracks on the browser.  I currently have five separate mRNA- 
Seq datasets that I have made tracks for, so I have used mRNA-Seq as  
the "method" in my gff3 file (i.e.,):

chr1    .       mRNA-Seq        4884     
100137802       .       .       .       Name=Sexual_IR_mRNA- 
Seq;Note=Sexual_IR_mRNA-Seq;wigfile=/Library/WebServer/Documents/ 
gbrowse/databases/Sme
d/wiggles/Sexual_IR_mRNA-Seq_001.chr1.1229636760.wig

I have entered separate track stanzas into my config file such as:

[track_001]
feature        = mRNA-Seq
glyph          = wiggle_xyplot
graph_type     = boxes
height         = 50
scale          = right
bgcolor        = blue
min_score      = 0
max_score      = 50
category       = mRNA-Seq
description    = mRNA-Seq from Sexual Nonirradiated
key            = Sexual_NIR-mRNA-Seq

[Sexual_IR_mRNA-Seq_001]
feature        = mRNA-Seq
glyph          = wiggle_xyplot
graph_type     = boxes
height         = 50
scale          = right
bgcolor        = blue
min_score      = 0
max_score      = 50
category       = mRNA-Seq
description    = mRNA-Seq from Sexual Irradiated
key            = Sexual_IR_mRNA-Seq

[Asexual_NIR_mRNA-Seq_001]
feature        = mRNA-Seq
glyph          = wiggle_xyplot
graph_type     = boxes
height         = 50
scale          = right
bgcolor        = blue
min_score      = 0
max_score      = 50
category       = mRNA-Seq
description    = mRNA-Seq from Asexual Nonirradiated

The problem is that all 5 wiggle tracks show up under the first of  
these.  How do I set things up so that each wiggle track has it's own  
separate box that can be checked on and off so that I can pick which  
data to view?  I guess I need to know which information in the config  
file calls the wiggle track file.

Thanks,

Brent








On Dec 18, 2008, at 4:35 PM, Smithies, Russell wrote:

> Does your gff file have a line pointing to the wiggle file?
> Are permissions correct to let GBrowse read the .wig file
>
> Eg.
> ##gff-version 3
> Chr4    .       brg_snps   1470    18578708        .       .
> .
> Name=brg%20associations;Note=snp%20associations%20in 
> %20arabidopsis;wigfile=/tmp/track_001.Chr4.1224712771.wig
>
>
>
> From: Brenton Graveley [mailto:brgraveley@...]
> Sent: Friday, 19 December 2008 7:06 a.m.
> To: gmod-gbrowse@...
> Subject: [Gmod-gbrowse] wiggle track won't display
>
> Hi,
>
> So, I have my chromosomes displaying now and am trying to install  
> wiggle tracks.
>
> I made wiggle tracks in the following format:
>
> track type=wiggle_0 name="Sexual_NIR-mRNA-Seq"  
> description="Sexual_NIR-mRNA-Seq" color=51,0,255 autoScale=on  
> visibility=full
> chr3    117     133     1
> chr3    133     152     2
> chr3    152     154     3
> chr3    154     158     4
> chr3    158     159     3
> chr3    159     165     4
> chr3    165     167     5
>
>
> I then ran:
>
> wiggle2gff3.pl --method=mRNA-Seq --path=/Library/WebServer/Documents/ 
> gbrowse/databases/Smed/wiggles 080806_Sexual_NIR_mRNA_bowtie.out.wig  
> > 080806_Sexual_NIR_mRNA.gff3
>
> Which gave this output:
>
> Processing 080806_Sexual_NIR_mRNA_bowtie.out.wig...wiggle file is  
> very large; resorting to genome-wide sample statistics at /Library/ 
> Perl/5.8.8/darwin-thread-multi-2level/Bio/Graphics/Wiggle/Loader.pm  
> line 345, <GEN0> line 2.
> loading wiggle into /Library/WebServer/Documents/gbrowse/databases/ 
> Smed/wiggles/track_001.chr3.1229612184.wig at /Library/Perl/5.8.8/ 
> darwin-thread-multi-2level/Bio/Graphics/Wiggle/Loader.pm line 571,  
> <GEN0> line 10002.
> loading wiggle into /Library/WebServer/Documents/gbrowse/databases/ 
> Smed/wiggles/track_001.chr4.1229612223.wig at /Library/Perl/5.8.8/ 
> darwin-thread-multi-2level/Bio/Graphics/Wiggle/Loader.pm line 571,  
> <GEN0> line 454765.
> loading wiggle into /Library/WebServer/Documents/gbrowse/databases/ 
> Smed/wiggles/track_001.chr7.1229612262.wig at /Library/Perl/5.8.8/ 
> darwin-thread-multi-2level/Bio/Graphics/Wiggle/Loader.pm line 571,  
> <GEN0> line 875126.
> loading wiggle into /Library/WebServer/Documents/gbrowse/databases/ 
> Smed/wiggles/track_001.chr2.1229612284.wig at /Library/Perl/5.8.8/ 
> darwin-thread-multi-2level/Bio/Graphics/Wiggle/Loader.pm line 571,  
> <GEN0> line 1146185.
> loading wiggle into /Library/WebServer/Documents/gbrowse/databases/ 
> Smed/wiggles/track_001.chr9.1229612330.wig at /Library/Perl/5.8.8/ 
> darwin-thread-multi-2level/Bio/Graphics/Wiggle/Loader.pm line 571,  
> <GEN0> line 1661602.
> loading wiggle into /Library/WebServer/Documents/gbrowse/databases/ 
> Smed/wiggles/track_001.chr8.1229612349.wig at /Library/Perl/5.8.8/ 
> darwin-thread-multi-2level/Bio/Graphics/Wiggle/Loader.pm line 571,  
> <GEN0> line 1870223.
> loading wiggle into /Library/WebServer/Documents/gbrowse/databases/ 
> Smed/wiggles/track_001.chr1.1229612366.wig at /Library/Perl/5.8.8/ 
> darwin-thread-multi-2level/Bio/Graphics/Wiggle/Loader.pm line 571,  
> <GEN0> line 2098795.
> loading wiggle into /Library/WebServer/Documents/gbrowse/databases/ 
> Smed/wiggles/track_001.chr6.1229612403.wig at /Library/Perl/5.8.8/ 
> darwin-thread-multi-2level/Bio/Graphics/Wiggle/Loader.pm line 571,  
> <GEN0> line 2607752.
> loading wiggle into /Library/WebServer/Documents/gbrowse/databases/ 
> Smed/wiggles/track_001.chr5.1229612431.wig at /Library/Perl/5.8.8/ 
> darwin-thread-multi-2level/Bio/Graphics/Wiggle/Loader.pm line 571,  
> <GEN0> line 2960089.
> done.
>
> After this, there were binaries in the wiggles directory as expected  
> and .gff file which I then loaded into the mysql database like this:
>
> bp_seqfeature_load.pl -d smed -f 080806_Sexual_NIR_mRNA.gff3
>
>
> I then added a track stanza to the config file:
>
> [mRNA-Seq]
> feature        = mRNA-Seq
> glyph          = wiggle_density
> height         = 50
> bgcolor        = blue
> category       = Genes
> description    = 1
> key            = Sexual_NIR-mRNA-Seq
>
> This track is now listed in the genes section of the tracks, but the  
> box is unchecked.  When i check the box and update the image, the  
> page refreshes without displaying the track on the browser, and the  
> track box is again unchecked.
>
> Seems as though it won't display for some reason.  ANy suggestions?
>
> Thanks,
>
> Brent
>
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