[Gmod-help] RE: [Gmod-gbrowse] selective feature display
Jayaraman, Pushkala
pjayaraman at mcw.edu
Thu Apr 8 17:53:18 EDT 2010
Hello,
Thanks for your response...On similar lines, I have another query:
I have a folder with SNP data totaling up to 288.0 Mb.All of this data will be ONE SINGLE TRACK on gbrowse2.
Now, I have atleast 10 other tracks being shown, including two "genes" track from different sources...so its a lot of data.
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.
I will be trying to load the snps onto a totally new database for improvement in speed to some extent.
apart from that I have already turned on slaves just for the snps.
(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.
I would lik eto knwo the following:
1. is "Semantic Zooming" the colution to this problem/
am I supposed to add any additional functions to the config file?
Apart from this I also will be loading another track with snps from another source which may be the same file size.
Thanks,
Pushkala
-----Original Message-----
From: gmodhelp at googlemail.com on behalf of Dave Clements, GMOD Help Desk
Sent: Thu 4/8/2010 2:07 PM
To: Jayaraman, Pushkala
Cc: gmod-gbrowse at lists.sourceforge.net
Subject: Re: [Gmod-gbrowse] selective feature display
Hi Pushkala,
I think you want:
http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Filtering_Search_Results
Dave C
On Fri, Apr 2, 2010 at 2:16 PM, Jayaraman, Pushkala <pjayaraman at mcw.edu>wrote:
> Hello,
> I was just re-reading the gbrowse tutorial where I came across this
> particular section:
>
>
> select
> This option gives you the ability to create a form of subtrack which the
> user can turn on and off. It is most suitable for tracks that have a few
> large features in them, such as genome-wide wiggle tracks. The form of
> the option is as follows:
> select = method value1 value2 value3'...
> method is one of name, display_name, type, source or score. This is
> followed by a list of selections that will be presented to the user to
> select among when he clicks on the "menu" icon in the track's title bar.
> For example, if you have a track in which the features have one of the
> sources "day 1" , "day 2", and "day 3", you can allow the user to select
> which of the features are visible with this option:
> select = source 'day 1' 'day 2' 'day 3'
> The matches are case insensitive regular expressions, so "day 1" will
> match "Day 1" and "DAY 1a".
>
>
>
>
> For a gff3 file such as this one:
> ##gff-version 3
> ##date Fri Apr 2 09:19:57 2010
> ##sequence-region chr1 1 267910886
> ##source gbrowse GFFDumper plugin
> ##NOTE: Selected features dumped.
> chr1 Hubrecht_Institute CNV 64749 1398577 . .
> .
> Dbxref=cnv_n1;strain=BN;type=Gain;method=Nimblegen+RN34+Whole+Genome+Til
> ing+Array
> chr1 Hubrecht_Institute CNV 55905520 55908133
> . . .
> Dbxref=cnv_a13;strain=BN-Lx;strain=SHR;strain=HXB2;strain=BXH3;type=Gain
> ;method=Affymetrix+RaEx+Rat+Exon+Array
> chr1 Hubrecht_Institute CNV 95469350 95471111
> . . .
> Dbxref=cnv_a29;strain=SS;strain=F344;strain=BS;strain=BN-Lx;strain=SHR;s
> train=HXB2;strain=BXH3;type=Gain;method=Affymetrix+RaEx+Rat+Exon+Array
> chr1 Hubrecht_Institute CNV 186040940 186042443
> . . .
> Dbxref=cnv_a45;strain=SS;strain=F344;strain=BN-Lx;strain=SHR;strain=HXB2
> ;strain=BXH3;type=Gain;method=Affymetrix+RaEx+Rat+Exon+Array
> chr1 Hubrecht_Institute CNV 228551935 228556303
> . . .
> Dbxref=cnv_a61;strain=SS;strain=Wis;strain=DA;strain=F344;strain=BS;stra
> in=COP;strain=LOU;strain=BS;strain=E3;strain=Wild;strain=BN-Lx;strain=SH
> R;strain=HXB2;strain=BXH3;type=Gain;method=Affymetrix+RaEx+Rat+Exon+Arra
> y
> chr1 Hubrecht_Institute CNV 112460322 112632348
> . . .
> Dbxref=cnv_w15;strain=SD;type=Gain;method=Whole+Genome+Shotgun+mapping
> chr1 Hubrecht_Institute CNV 37913670 37915915
> . . .
> Dbxref=cnv_a10;type=Loss;method=Affymetrix+RaEx+Rat+Exon+Array
> chr1 Hubrecht_Institute CNV 80041360 80044509
> . . .
> Dbxref=cnv_a26;strain=SS;strain=Wis;strain=DA;strain=F344;strain=BS;stra
> in=COP;strain=LOU;strain=BS;strain=E3;strain=Wild;strain=BN-Lx;strain=SH
> R;strain=HXB2;strain=BXH3;type=Gain;method=Affymetrix+RaEx+Rat+Exon+Arra
> y
> chr1 Hubrecht_Institute CNV 178083566 178087252
> . . .
> Dbxref=cnv_a42;strain=SS;strain=Wis;strain=DA;strain=BS;strain=COP;strai
> n=LOU;strain=BS;strain=E3;strain=Wild;strain=SHR;strain=HXB2;strain=BXH3
> ;type=Loss;method=Affymetrix+RaEx+Rat+Exon+Array
>
>
>
>
> is there any way to use the "select" method on the attributes such that
> it we can selectively display features only under certain attributes?
> For eg: in the above gff3 file there are multiple "strain" values. What
> if we only wanted to display only those that had strain=BXH3
>
> Would that be possible? and How?
>
>
> Pushkala
>
>
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