Rayapadi Swetha | 4 Mar 12:59 2015
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Fwd: Need a help


Dear Sir,

Tons of thanks. I followed your suggestion, option 2. Now it works well. You helped me a lot in GBrowse (Starting from installation to till now). Thank you so much. I used GBrowse in two databases and both are published. One in Genomics and other in Computers in Biology and Medicine. This publication is not possible without your guidance.

Thank you.

Yours sincerely,
Swetha R G,
Research Associate,
School of BioSciences and Technology,
VIT University,
India.

On Thu, Nov 27, 2014 at 9:27 AM, Rayapadi Swetha <swetha.rayapadi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear Sir,

Thank you so much for your quick reply. Let me work according to your suggestion and If I stuck at any point, Please help me.

Yours sincerely,
Swetha R G.

On Wed, Nov 26, 2014 at 9:53 PM, Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> wrote:
Hi Swetha,

The only way I can think of to do that is with separate configuration files for GBrowse unfortunately.  The "data source" drop down was originally conceived of to allow selecting different "species", but that concept doesn't map very well to strains of a virus.  There are two approaches I could see using:

1. Revamp the way you're using GBrowse data sources altogether, so that each data source represents one type of virus, so in the drop down you'd have two entries, one for H. influenzae and one for the other virus.  Each strain would then be analogous a chromosome. One advantage to this approach is that when/if you have hundreds of strains of a virus the drop down will still be useable (that is, a drop down menu with a more than 20-30 entries is very unwieldy).  Users would be able to use the search box to find strains they are interested in.  A potential downside is that searching for a particular gene would yield results for that gene in every strain.

2. Create separate gbrowse2 config directories for each virus.  Then you need to edit gbrowse2.conf file that lives in the apache configuration; where that is varies depending on your OS; on Ubuntu 12.04 it's in /etc/apache2/conf.d/.  You'll need separate cgi-bin directories too, for example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and /usr/lib/cgi-bin/Segb2 for the Something else virus :-)  In the apache gbrowse.conf file you need separate entries for the different cgi-bin directores that have different "SetEnv GBROWSE_CONF" entries to point at the separate gbrowse config directories.

Obviously, it's up to you to decide which is better; there will be work either way.  I suggest that if you choose the second path that you make very incremental changes and test that GBrowse still works all along the way, because there are several moving parts that could break GBrowse and with the changes required, it might be difficult to sort out what happened if something goes wrong.

Scott


On Wed, Nov 26, 2014 at 10:13 AM, Rayapadi Swetha <swetha.rayapadi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Respected Sir,

We have developed a database for Haemophilus influenzae and we used Gbrowse to visualize their annotation. Now, we are developing the database for other organism and we need to use the Gbrowse. We are going to host the second database in the same server where GBrowse is already installed. But, I have a doubt. The dropdown menu for the second database should be changed in GBrowse. How is it possible?

For example:

In Haemophilus influenzae database, we have included 10 different strains of H. influenzae. I have attached the screenshot for your reference.

In second database, I need to include 25 strains of other organism.

Query: these 25 strains should be in dropdown menu instead of those 10 strains. And, When the user access H. influenzae database, 10 strains should be there and when the user access second database, 25 strains should be there. How is it possible?

Waiting for your reply.

Yours sincerely,
Swetha R G.



--
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Ontario Institute for Cancer Research



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Scott Cain | 4 Mar 15:14 2015
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Re: Need a help

Hi Swetha,

Please always ask questions on the mailing list (cc'ed here).

If you are using fastcgi, you may need to restart apache to recognize the change you made in your config file.  The other possibility is that you didn't really edit the config file that GBrowse is using (believe me, I've done that many times, where I edit a copy of the config file and can't understand why it isn't having any effect).

Scott


On Wed, Mar 4, 2015 at 6:58 AM, Rayapadi Swetha <swetha.rayapadi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear Sir,

I have a doubt in Gbrowse. Can you please help me sir?

Herewith, I have attached the conf file.


It works well in Browser. In file, suppose, If I change initial landmark = NC_022659.1:1..10000 to initial landmark = NC_022659.1:20639..15623, the browser displays the old landmark itself (i.e 1..10000). I know its because of some cache problem. If I delete the browser history, then the browser displays the new landmark. Can you please solve this issue?

Yours sincerely,
Swetha R G,
Senior Research Fellow (ICMR),
VIT University,
Vellore,
India.








On Thu, Nov 27, 2014 at 8:21 PM, Rayapadi Swetha <swetha.rayapadi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear Sir,

Tons of thanks. I followed your suggestion, option 2. Now it works well. You helped me a lot in GBrowse (Starting from installation to till now). Thank you so much. I used GBrowse in two databases and both are published. One in Genomics and other in Computers in Biology and Medicine. This publication is not possible without your guidance.

Thank you.

Yours sincerely,
Swetha R G,
Research Associate,
School of BioSciences and Technology,
VIT University,
India.

On Thu, Nov 27, 2014 at 9:27 AM, Rayapadi Swetha <swetha.rayapadi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear Sir,

Thank you so much for your quick reply. Let me work according to your suggestion and If I stuck at any point, Please help me.

Yours sincerely,
Swetha R G.

On Wed, Nov 26, 2014 at 9:53 PM, Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> wrote:
Hi Swetha,

The only way I can think of to do that is with separate configuration files for GBrowse unfortunately.  The "data source" drop down was originally conceived of to allow selecting different "species", but that concept doesn't map very well to strains of a virus.  There are two approaches I could see using:

1. Revamp the way you're using GBrowse data sources altogether, so that each data source represents one type of virus, so in the drop down you'd have two entries, one for H. influenzae and one for the other virus.  Each strain would then be analogous a chromosome. One advantage to this approach is that when/if you have hundreds of strains of a virus the drop down will still be useable (that is, a drop down menu with a more than 20-30 entries is very unwieldy).  Users would be able to use the search box to find strains they are interested in.  A potential downside is that searching for a particular gene would yield results for that gene in every strain.

2. Create separate gbrowse2 config directories for each virus.  Then you need to edit gbrowse2.conf file that lives in the apache configuration; where that is varies depending on your OS; on Ubuntu 12.04 it's in /etc/apache2/conf.d/.  You'll need separate cgi-bin directories too, for example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and /usr/lib/cgi-bin/Segb2 for the Something else virus :-)  In the apache gbrowse.conf file you need separate entries for the different cgi-bin directores that have different "SetEnv GBROWSE_CONF" entries to point at the separate gbrowse config directories.

Obviously, it's up to you to decide which is better; there will be work either way.  I suggest that if you choose the second path that you make very incremental changes and test that GBrowse still works all along the way, because there are several moving parts that could break GBrowse and with the changes required, it might be difficult to sort out what happened if something goes wrong.

Scott


On Wed, Nov 26, 2014 at 10:13 AM, Rayapadi Swetha <swetha.rayapadi <at> gmail.com> wrote:
Respected Sir,

We have developed a database for Haemophilus influenzae and we used Gbrowse to visualize their annotation. Now, we are developing the database for other organism and we need to use the Gbrowse. We are going to host the second database in the same server where GBrowse is already installed. But, I have a doubt. The dropdown menu for the second database should be changed in GBrowse. How is it possible?

For example:

In Haemophilus influenzae database, we have included 10 different strains of H. influenzae. I have attached the screenshot for your reference.

In second database, I need to include 25 strains of other organism.

Query: these 25 strains should be in dropdown menu instead of those 10 strains. And, When the user access H. influenzae database, 10 strains should be there and when the user access second database, 25 strains should be there. How is it possible?

Waiting for your reply.

Yours sincerely,
Swetha R G.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research






--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Sam Hokin | 4 Mar 05:34 2015

Search on load_id attribute (Ensembl genomes)?

Hi, folks, just joined the list after spending a lot of time with GBrowse the past few months. My question: Is
there any way to get 
search to search on the load_id attribute?

Annotated genes that I get from the Ensembl plant database (I'm working with the maize AGPv3 genome, aka
B73_RefGen_v3) do not have 
a Name attribute in the GFF3 file. Here's a typical line from Zea_mays.AGPv3.24.gff3 (swapping spaces for tabs):

10 ensembl gene 28054052 28054433 . + .
ID=gene:GRMZM5G846142;assembly_name=AGPv3;biotype=protein_coding;description=Uncharacterized 
protein  [Source:UniProtKB/TrEMBL%3BAcc:K7TYI5];logic_name=genebuilder;version=1

A lot of wonderful info there in the attributes, but no Name is provided. This gets loaded into my database
(using 
bp_seqfeature_load.pl) with load_id=gene:GRMZM5G846142 and no Name. If one searches for
"GRMZM5G846142" or "gene:GRMZM5G846142" in 
the browser, one gets Not Found. (Oddly, Ensembl does provide a Name attribute for exons; but not genes,
transcripts or CDS, at 
least in the current version - and by the way, the color-coded GFF3 parent-child relationship display
works wonderfully with those!)

Yes, I can futz with the GFF file, or run a SQL script to insert a record in name for all load_id records in
attributes that don't 
have one in name, and all sorts of things, but I thought maybe there's a way to avoid that in a conf file.
Ensembl is a pretty big 
source of genome data, so I'd think this would come up a lot.

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Vladimir Gritsenko | 2 Mar 11:36 2015
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Best way to present a copy number variation track?

Hi all,

I’m writing a CNV track, which I’m representing as a histogram (~5 kbp per each bar), in GFF3. Here’s
what I need:

1) Y scales that will always be present to the left and the right of the track.
2) Horizontal lines running along pre-set Y values.
3) Each bar in the histogram labeled with its value.

To break down each question I have:

1) The biggest issue I’ve had is the Y scales. In GFF3, if I don’t aggregate my data points, I get a lot of
scale cartoons, cluttering the view when zooming out. If I do aggregate my views, the scales will only be
presented at the beginning, middle and end of the chromosome - that’s too sparse. Ideally, I would like
the scales to be presented in a zoom-invariant way - always to the left, right and maybe middle of the
visible portion of the track.
2) The second issue is the horizontal lines. I think I can just add a feature to represent that line, but the
problem with it being a feature is that users may click on it by mistake (instead of the histogram bar).
Also, if it’s not marked, it loses its effect without scales.
3) I’ve found no way to label each individual bar. I did manage to have the CNV value be in the mouse-hover
balloon (via the $description variable).

I think that 1+2 and 3 are mutually exclusive in terms of necessary features - that is, if the scale question
is undoable but the labeling is doable, that may be good enough, and vice versa.

Any other thoughts or examples on how to represent CNV tracks will be greatly appreciated.

Thank you!
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Atanas Kumbarov | 28 Feb 22:55 2015
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Export from the ISOGG YBrowse is broken

Hi,
I am trying to export data from the ISOGG YBrowse at http://ybrowse.y-chromosome.org/gb2/gbrowse/chrY/ but export seems to be broken. I always get this error:

# The landmark named ChrY:NaN..NaN was not found.
Your e-mail address was given for technical support.

Best regards,
Atanas Kumbarov

http://www.kumbarov.com
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Vladimir Gritsenko | 25 Feb 17:28 2015
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FFF multiple sequence ID issue

Hello all,

I’m having a problem with an FFF file. It defines an xyplot histogram, and includes multiple sequence
IDs. However, GBrowse 2.49 (as deployed on CGD) files all features under the first sequence ID it
encounters, and ignored the rest.

This leads to me another question. Is there a “canonical" version of GBrowse against which potential
bugs can be tested?

The test data is:

[CNV]
glyph = xyplot
graph_type=histogram
fgcolor = black
bgcolor = black
height=50
min_score=0
max_score=4
label=1
key=CNV histogram

CNV	" "	Ca21chr1_C_albicans_SC5314:1..5000	score=4

CNV	" "	Ca21chr2_C_albicans_SC5314:1..5000	score=3

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Vaneet Lotay | 23 Feb 23:02 2015
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CDS and exon segments

Hello all,

 

Lately I’ve been getting a lot of GFF3 files with both CDS and exon segments linked to each mRNA segment with a child-parent relationship.  The only thing is sometimes but not every time the CDS segments will not perfectly overlap with the stop positions of the mRNA and the matching exons.  Usually the last exon does perfectly overlap with the end of the mRNA from what I’ve found.  What I’m curious is how GBrowse compiles or reads these GFF3 files with both these segments because clearly it doesn’t draw both CDS and exons.  Does it only look for one of the keywords?  If you removed all CDS segments would it still draw the mRNA in exon/intron transcript style?

 

Thanks,

 

Vaneet

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Simon Deroles | 20 Feb 03:42 2015
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Finding contig or scaffold location in GBrowse

Hi There

Please forgive me if this is a stupid question.  I am looking at the Kiwifruit genome database at http://bioinfo.bti.cornell.edu/cgi-bin/kiwi/home.cgi.

I have used BLAST to find a seq of interest and it is able to locate the seq on either a scaffold location or config location.  I now want to look at the flanking regions around this seq but am unable to use the scaffold or config indentifiers to go to their location in Gbrowse.  How do i find the reverent region in Gbrowse?  The BLAST results do not return a gene name or chromosome location.

Many thanks for your help

Kind Regards

Simon Deroles
Simon Deroles
Senior Scientist



 

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Thomas LETELLIER | 16 Feb 14:57 2015
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outsource passwords of GBrowse configuration files

Hi,

I use Git with my GBrowse configuration files, I would like to avoid to 
put passwords into Git. Do you know if there is a way to store passwords 
elsewhere ? (in a dedicated file for example).

Best regards,

Thomas

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Vladimir Gritsenko | 12 Feb 15:23 2015
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Different display properties for different objects in the track?

Hello all,

I’m working with CGD’s GBrowse (2.49). I want to create a track of SNPs (and for this I’m using
“glyph=triangle”), where each SNP (triangle) may have one of a predefined list of colours. So, while
I can set “bgcolor” for the entire track, this isn’t good enough. I tried using Perl callbacks, but
this doesn’t seem to work for CGD’s GBrowse instance. Is this possible, and if yes, how?

Thank you in advance,
Vladimir Gritsenko
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Vaneet Lotay | 5 Feb 00:19 2015
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Render error: illegal division by zero

I was trying to load several BigWig files from an external collaborator into our GBrowse and some of them displayed correctly while some of them couldn’t display correctly due to an error.  The ones that didn’t load all came up with this error:

 

…..rendering error track: Illegal division by zero at /usr/local/share/perl5/Bio/Graphics/Glyph/wiggle_data.pm line 420. at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 3693., referer: http://.....

 

I have successfully installed the Bio::DB::BigWig and Bio::DB::BigWigSet modules so there’s nothing wrong there.  Even if I change the glyph, the exact same error occurs except in that respective graph module instead of wiggle_data.pm.  I unpacked some of these BigWig files to see their contents and it appears they more closely follow a bedGraph format as opposed to wiggle:

 

#bedGraph section Chr01:82-481773

Chr01                                                                                                                                          82      242         0.147608

Chr01                                                                                                                                          446   466         0.147608

Chr01                                                                                                                                          466   606         0.295216

Chr01                                                                                                                                          606   626         0.147608

Chr01                                                                                                                                          1267 1427       0.147608

Chr01                                                                                                                                          1782 1942       0.147608

Chr01                                                                                                                                          6055 6076       0.147608

Chr01                                                                                                                                          6076 6213       0.295216

…….

 

No header line is present in any of these files which is also weird as I thought that was required but it doesn’t seem to affect the display of the other BigWig files which have an identical format underneath.  I’m thinking it must be something in the content of the file but nothing obvious stands out and there isn’t really a pattern to the files that do display and those that don’t.

 

Please help if any of you have encountered this error before.

 

Thanks,

 

Vaneet

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