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<P><FONT SIZE=2>Hello,<BR>
Thanks for your response...On similar lines, I have another query:<BR>
<BR>
I have a folder with SNP data totaling up to 288.0 Mb.All of this data will be ONE SINGLE TRACK on gbrowse2.<BR>
Now, I have atleast 10 other tracks being shown, including two "genes" track from different sources...so its a lot of data.<BR>
I realize that my system seems to slow down while rendering tracks.. I am not able to render the SNP track when I choose the whole chromosome view. I am only able to visualize snps when I zoom into a region less than 1MB in size.<BR>
<BR>
I will be trying to load the snps onto a totally new database for improvement in speed to some extent.<BR>
apart from that I have already turned on slaves just for the snps.<BR>
<BR>
(It took me 20 minutes to write this email as the system had stopped responding because I tried to look at snps in a region greater than 10 Mb. I can safely say that 1Mb is a clear region for viewing snps. After this, the glyphs start to clump together and showthemselves as a big dark patch.<BR>
<BR>
I would lik eto knwo the following:<BR>
1. is "Semantic Zooming" the colution to this problem/<BR>
<BR>
am I supposed to add any additional functions to the config file?<BR>
<BR>
<BR>
Apart from this I also will be loading another track with snps from another source which may be the same file size.<BR>
<BR>
Thanks,<BR>
Pushkala<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmodhelp@googlemail.com on behalf of Dave Clements, GMOD Help Desk<BR>
Sent: Thu 4/8/2010 2:07 PM<BR>
To: Jayaraman, Pushkala<BR>
Cc: gmod-gbrowse@lists.sourceforge.net<BR>
Subject: Re: [Gmod-gbrowse] selective feature display<BR>
<BR>
Hi Pushkala,<BR>
<BR>
I think you want:<BR>
<A HREF="http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Filtering_Search_Results">http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Filtering_Search_Results</A><BR>
<BR>
Dave C<BR>
<BR>
On Fri, Apr 2, 2010 at 2:16 PM, Jayaraman, Pushkala <pjayaraman@mcw.edu>wrote:<BR>
<BR>
> Hello,<BR>
> I was just re-reading the gbrowse tutorial where I came across this<BR>
> particular section:<BR>
><BR>
><BR>
> select<BR>
> This option gives you the ability to create a form of subtrack which the<BR>
> user can turn on and off. It is most suitable for tracks that have a few<BR>
> large features in them, such as genome-wide wiggle tracks. The form of<BR>
> the option is as follows:<BR>
> select = method value1 value2 value3'...<BR>
> method is one of name, display_name, type, source or score. This is<BR>
> followed by a list of selections that will be presented to the user to<BR>
> select among when he clicks on the "menu" icon in the track's title bar.<BR>
> For example, if you have a track in which the features have one of the<BR>
> sources "day 1" , "day 2", and "day 3", you can allow the user to select<BR>
> which of the features are visible with this option:<BR>
> select = source 'day 1' 'day 2' 'day 3'<BR>
> The matches are case insensitive regular expressions, so "day 1" will<BR>
> match "Day 1" and "DAY 1a".<BR>
><BR>
><BR>
><BR>
><BR>
> For a gff3 file such as this one:<BR>
> ##gff-version 3<BR>
> ##date Fri Apr 2 09:19:57 2010<BR>
> ##sequence-region chr1 1 267910886<BR>
> ##source gbrowse GFFDumper plugin<BR>
> ##NOTE: Selected features dumped.<BR>
> chr1 Hubrecht_Institute CNV 64749 1398577 . .<BR>
> .<BR>
> Dbxref=cnv_n1;strain=BN;type=Gain;method=Nimblegen+RN34+Whole+Genome+Til<BR>
> ing+Array<BR>
> chr1 Hubrecht_Institute CNV 55905520 55908133<BR>
> . . .<BR>
> Dbxref=cnv_a13;strain=BN-Lx;strain=SHR;strain=HXB2;strain=BXH3;type=Gain<BR>
> ;method=Affymetrix+RaEx+Rat+Exon+Array<BR>
> chr1 Hubrecht_Institute CNV 95469350 95471111<BR>
> . . .<BR>
> Dbxref=cnv_a29;strain=SS;strain=F344;strain=BS;strain=BN-Lx;strain=SHR;s<BR>
> train=HXB2;strain=BXH3;type=Gain;method=Affymetrix+RaEx+Rat+Exon+Array<BR>
> chr1 Hubrecht_Institute CNV 186040940 186042443<BR>
> . . .<BR>
> Dbxref=cnv_a45;strain=SS;strain=F344;strain=BN-Lx;strain=SHR;strain=HXB2<BR>
> ;strain=BXH3;type=Gain;method=Affymetrix+RaEx+Rat+Exon+Array<BR>
> chr1 Hubrecht_Institute CNV 228551935 228556303<BR>
> . . .<BR>
> Dbxref=cnv_a61;strain=SS;strain=Wis;strain=DA;strain=F344;strain=BS;stra<BR>
> in=COP;strain=LOU;strain=BS;strain=E3;strain=Wild;strain=BN-Lx;strain=SH<BR>
> R;strain=HXB2;strain=BXH3;type=Gain;method=Affymetrix+RaEx+Rat+Exon+Arra<BR>
> y<BR>
> chr1 Hubrecht_Institute CNV 112460322 112632348<BR>
> . . .<BR>
> Dbxref=cnv_w15;strain=SD;type=Gain;method=Whole+Genome+Shotgun+mapping<BR>
> chr1 Hubrecht_Institute CNV 37913670 37915915<BR>
> . . .<BR>
> Dbxref=cnv_a10;type=Loss;method=Affymetrix+RaEx+Rat+Exon+Array<BR>
> chr1 Hubrecht_Institute CNV 80041360 80044509<BR>
> . . .<BR>
> Dbxref=cnv_a26;strain=SS;strain=Wis;strain=DA;strain=F344;strain=BS;stra<BR>
> in=COP;strain=LOU;strain=BS;strain=E3;strain=Wild;strain=BN-Lx;strain=SH<BR>
> R;strain=HXB2;strain=BXH3;type=Gain;method=Affymetrix+RaEx+Rat+Exon+Arra<BR>
> y<BR>
> chr1 Hubrecht_Institute CNV 178083566 178087252<BR>
> . . .<BR>
> Dbxref=cnv_a42;strain=SS;strain=Wis;strain=DA;strain=BS;strain=COP;strai<BR>
> n=LOU;strain=BS;strain=E3;strain=Wild;strain=SHR;strain=HXB2;strain=BXH3<BR>
> ;type=Loss;method=Affymetrix+RaEx+Rat+Exon+Array<BR>
><BR>
><BR>
><BR>
><BR>
> is there any way to use the "select" method on the attributes such that<BR>
> it we can selectively display features only under certain attributes?<BR>
> For eg: in the above gff3 file there are multiple "strain" values. What<BR>
> if we only wanted to display only those that had strain=BXH3<BR>
><BR>
> Would that be possible? and How?<BR>
><BR>
><BR>
> Pushkala<BR>
><BR>
><BR>
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