[Gmod-help] RE: [Gmod-gbrowse] Create SNP density track
Jayaraman, Pushkala
pjayaraman at mcw.edu
Mon Apr 26 13:52:05 EDT 2010
Thank you J
From: Lincoln Stein [mailto:lincoln.stein at gmail.com]
Sent: Monday, April 26, 2010 12:51 PM
To: Jayaraman, Pushkala
Cc: Dave Clements, GMOD Help Desk; Wes Barris;
gmod-gbrowse at lists.sourceforge.net
Subject: Re: [Gmod-help] RE: [Gmod-gbrowse] Create SNP density track
That's right.
Lincoln
On Mon, Apr 26, 2010 at 1:49 PM, Jayaraman, Pushkala
<pjayaraman at mcw.edu> wrote:
So all that I have to do is generate histograms in GFF and use
Bio::DB::GFF in the conf file for this track instead?
Pushkala
From: gmodhelp at googlemail.com [mailto:gmodhelp at googlemail.com] On Behalf
Of Dave Clements, GMOD Help Desk
Sent: Monday, April 26, 2010 12:32 PM
To: Jayaraman, Pushkala
Cc: Wes Barris; gmod-gbrowse at lists.sourceforge.net
Subject: Re: [Gmod-gbrowse] Create SNP density track
Hi Pushkala,
I don't believe there is any difference between how this is handled in
the two different versions of GBrowse.
Dave C
On Mon, Apr 19, 2010 at 11:30 PM, Jayaraman, Pushkala
<pjayaraman at mcw.edu> wrote:
Hello,
This may be a repeat question:
Is the command on gbrowse2 different or creating snp density track?
In gbrowse1.7:
========================================================================
========================================
Generating Feature Frequency histograms
Note: this applies to GFF2 databases only and needs to be rewritten
slightly for GFF3
With a little bit of additional effort, you can set one or more tracks
up to display a density histogram of the features contained within the
track. For example, the human data source in the GBrowse demo uses
density histograms in the chromosomal overview. In addition, when the
features in the SNP track become too dense to view, this track converts
into a histogram. To see this in action, turn on the SNP track and then
zoom out beyond 150K - Link plz?
There are four steps for making histograms:
generate the density data using the bp_generate_histogram.pl script.
load the density data using bp_load_gff.pl or bp_fast_load_gff.pl.
declare a density aggregator to the gbrowse configuration file
add the density aggregator to the appropriate track in the configuration
file.
The first step is to generate the density data. Currently this is done
by generating a GFF file containing a set of "bin" feature types. Use
the bp_generate_histogram.pl script to do this. You will find it in
BioPerl under the scripts/Bio-DB-GFF directory.
Assuming that your database is named "dicty", you have a feature named
SNP, and you wish to generate a density distribution across 10,000 bp
bins, here is the command you would use:
bp_generate_histogram.pl -merge -d dicty -bin 10000 SNP
>snp_density.gff
This is saying to use the "dicty" database (-d) option, to use 10,000 bp
bins (the -bin option) and to count the occurrences of the SNP feature
throughout the database. In addition, the -merge option says to merge
all types of SNPs into a single bin. Otherwise they will be stratified
by their source. The resulting GFF file contains a series of entries
like these ones:
Chr1 SNP bin 1 10000 49 + . bin Chr1:SNP
Chr1 SNP bin 10001 20000 29 + . bin Chr1:SNP
What this is saying is that there are now a series of pseudo-features of
type "bin:SNP" that occupy successive 10,000 bp regions of the genome.
The score field contains the number of times a SNP was seen in that bin.
You'll now load this file using bp_load_gff.pl or bp_fast_load_gff.pl:
bp_load_gff.pl -d dicty snp_density.gff
The next step is to tell GBrowse how to use this information. You do
this by creating a new aggregator for the SNP density information. Open
the GBrowse configuration file and find the aggregators option. Add a
new aggregator that looks like this:
aggregators = snp_density{bin:SNP}
This is declaring a new feature named "snp_density" that is composed of
subparts of type bin:SNP.
The last step is to declare a track for the density information. You
will use the "xyplot" glyph, which can draw a number of graphs,
including histograms. To add the SNP density information as a static
track in the overview, create a section like this one:
[SNP:overview]
feature = snp_density
glyph = xyplot
graph_type = boxes
scale = right
bgcolor = red
fgcolor = red
height = 20
key = SNP Density
This is declaring a new constant track in the overview named "SNP
Density." The feature is "snp_density", corresponding to the aggregator
declared earlier. The glyph is "xyplot" using the graph type of "boxes"
to generate a column graph.
To set up a track so that the histogram appears when the user zooms out
beyond 100,000 bp but shows the detailed information at higher
magnifications, generate two track sections like these:
[SNPs]
feature = snp
glyph = triangle
point = 1
orient = N
height = 6
bgcolor = blue
fgcolor = blue
key = SNPs
[SNPs:100000]
feature = snp_density
glyph = xyplot
graph_type = boxes
scale = right
The first track section sets up the defaults for the SNP track. SNPs are
represented as blue triangles pointing North. The second track
declaration declares that when the user zooms out to over 100K base
pairs, GBrowse should display the snp_density feature using the xyplot
glyph.
========================================================================
=============================
How different is this for gbrowse2?
Pushkala
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Lincoln D. Stein
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