snp data into gff

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snp data into gff

Nikhat Zafar
Hi,

 I would like to display snps as they are shown in this gbrowse instance :
http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/hapmap27_B36/?name=SNP%3Ars6870660.
My question is  how to format data  in gff to have a display like hapmap.

 Nikhat

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Re: snp data into gff

Jayaraman, Pushkala
Hi Nikhat,
You will need to create snp density track.
There is a bp_generate_histogram.pl script that will help you do that.
Check out:
"Generating Feature Frequency histograms" under
http://gmod.org/wiki/GBrowse_Configuration_HOWTO

You will get your answer

Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu

-----Original Message-----
From: Nikhat Zafar [mailto:[hidden email]]
Sent: Tuesday, June 01, 2010 10:56 AM
To: Gbrowse Mailing List
Subject: [Gmod-gbrowse] snp data into gff

Hi,

 I would like to display snps as they are shown in this gbrowse instance
:
<a href="http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/hapmap27_B36/?name=SNP%3">http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/hapmap27_B36/?name=SNP%3
Ars6870660.
My question is  how to format data  in gff to have a display like
hapmap.

 Nikhat

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gbrowse_syn question

Jayaraman, Pushkala
Hello,
I seem to be having problems getting the synteny viewer to work with the
sample dataset
This is the protocol I followed:
1. set up the databases in mysql. I created rice, wild_rice and
rice_synteny databases on the mysql databases I gave them all insert and
select privileges.
2. I ran the bp_seqfeature_load.pl on the rice.gff3 and the
wild_rice.gff3 files to load them into their respective databases like
this:

*bp_seqfeature_load.pl -u gbrowser -p [pass] -d
'DBI:mysql:database=wild_rice;host=forte.hmgc.mcw.edu;mysql_local_infile
=1' -c -f ../wild_rice/wild_rice.gff3

*bp_seqfeature_load.pl -u gbrowser -p [pass] -d
'DBI:mysql:database=rice;host=forte.hmgc.mcw.edu;mysql_local_infile=1'
-c -f ../rice/rice.gff3

3. I also ran the gbrowse_syn_load_alignments_msa.pl -u gbrowser -p
gbr12ws4 -d 'DBI:mysql:database=rice_synteny;host=forte.hmgc.mcw.edu' -c
-v rice.aln  

I modified the .conf files and the .synconf file to point to the mysql
database. And yet I get the "No data source" message. This is what the
apache error logs mention..


[Tue Jun 01 14:10:26 2010] [error] [client 141.106.161.52] [Tue Jun  1
14:10:26 2010] gbrowse_syn: Use of uninitialized value in concatenation
(.) or string at /usr/local/apache2
/cgi-bin/gbrowse_syn line 9, <DATA> line 192.


Where have I gone wrong?
Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu

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Re: snp data into gff

Dave Clements, GMOD Help Desk-3
In reply to this post by Nikhat Zafar
Hi Nikhat,

Which part of the display do you want to emulate?  The coverage, the genotype frequencies, or something else?  The coverage tracks are probably represented in wig files (see http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html?content-type=text%2Fhtml#wiggle).  The genotype frequency bars are generated with the allele_column_multi glyph.  This used to be available for download from the Hapmap site, but the address I have no longer works (and I've cc'd their help person).  If that is not immediately available, I think you can do similar things with the stackedplot glyph.  See http://gmod.svn.sourceforge.net/viewvc/gmod/Bio-Graphics/trunk/lib/Bio/Graphics/Glyph/stackedplot.pm?view=markup&sortby=file.

Dave C.

On Tue, Jun 1, 2010 at 8:55 AM, Nikhat Zafar <[hidden email]> wrote:
Hi,

 I would like to display snps as they are shown in this gbrowse instance :
http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/hapmap27_B36/?name=SNP%3Ars6870660.
My question is  how to format data  in gff to have a display like hapmap.

 Nikhat

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