<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 12 (filtered medium)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Wingdings;
panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Wingdings;
panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.Section1
{page:Section1;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang=EN-US link=blue vlink=purple>
<div class=Section1>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thank you </span><span style='font-size:11.0pt;font-family:Wingdings;
color:#1F497D'>J</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Lincoln Stein
[mailto:lincoln.stein@gmail.com] <br>
<b>Sent:</b> Monday, April 26, 2010 12:51 PM<br>
<b>To:</b> Jayaraman, Pushkala<br>
<b>Cc:</b> Dave Clements, GMOD Help Desk; Wes Barris;
gmod-gbrowse@lists.sourceforge.net<br>
<b>Subject:</b> Re: [Gmod-help] RE: [Gmod-gbrowse] Create SNP density track<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>That's right.<o:p></o:p></p>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'>Lincoln<o:p></o:p></p>
<div>
<p class=MsoNormal>On Mon, Apr 26, 2010 at 1:49 PM, Jayaraman, Pushkala <<a
href="mailto:pjayaraman@mcw.edu">pjayaraman@mcw.edu</a>> wrote:<o:p></o:p></p>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='font-size:11.0pt;color:#1F497D'>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?</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='font-size:11.0pt;color:#1F497D'> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='font-size:11.0pt;color:#1F497D'>Pushkala</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='font-size:11.0pt;color:#1F497D'> </span><o:p></o:p></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span
style='font-size:10.0pt'>From:</span></b><span style='font-size:10.0pt'> <a
href="mailto:gmodhelp@googlemail.com" target="_blank">gmodhelp@googlemail.com</a>
[mailto:<a href="mailto:gmodhelp@googlemail.com" target="_blank">gmodhelp@googlemail.com</a>]
<b>On Behalf Of </b>Dave Clements, GMOD Help Desk<br>
<b>Sent:</b> Monday, April 26, 2010 12:32 PM<br>
<b>To:</b> Jayaraman, Pushkala<br>
<b>Cc:</b> Wes Barris; <a href="mailto:gmod-gbrowse@lists.sourceforge.net"
target="_blank">gmod-gbrowse@lists.sourceforge.net</a><br>
<b>Subject:</b> Re: [Gmod-gbrowse] Create SNP density track</span><o:p></o:p></p>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hi
Pushkala,<o:p></o:p></p>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I
don't believe there is any difference between how this is handled in the two
different versions of GBrowse.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'>Dave C<o:p></o:p></p>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>On
Mon, Apr 19, 2010 at 11:30 PM, Jayaraman, Pushkala <<a
href="mailto:pjayaraman@mcw.edu" target="_blank">pjayaraman@mcw.edu</a>>
wrote:<o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hello,<br>
This may be a repeat question:<br>
<br>
Is the command on gbrowse2 different or creating snp density track?<br>
In gbrowse1.7:<br>
========================================================================<br>
========================================<br>
<br>
Generating Feature Frequency histograms<br>
<br>
Note: this applies to GFF2 databases only and needs to be rewritten<br>
slightly for GFF3<br>
With a little bit of additional effort, you can set one or more tracks<br>
up to display a density histogram of the features contained within the<br>
track. For example, the human data source in the GBrowse demo uses<br>
density histograms in the chromosomal overview. In addition, when the<br>
features in the SNP track become too dense to view, this track converts<br>
into a histogram. To see this in action, turn on the SNP track and then<br>
zoom out beyond 150K - Link plz?<br>
There are four steps for making histograms:<br>
generate the density data using the <a href="http://bp_generate_histogram.pl"
target="_blank">bp_generate_histogram.pl</a> script.<br>
load the density data using <a href="http://bp_load_gff.pl" target="_blank">bp_load_gff.pl</a>
or <a href="http://bp_fast_load_gff.pl" target="_blank">bp_fast_load_gff.pl</a>.<br>
declare a density aggregator to the gbrowse configuration file<br>
add the density aggregator to the appropriate track in the configuration<br>
file.<br>
The first step is to generate the density data. Currently this is done<br>
by generating a GFF file containing a set of "bin" feature types. Use<br>
the <a href="http://bp_generate_histogram.pl" target="_blank">bp_generate_histogram.pl</a>
script to do this. You will find it in<br>
BioPerl under the scripts/Bio-DB-GFF directory.<br>
Assuming that your database is named "dicty", you have a feature
named<br>
SNP, and you wish to generate a density distribution across 10,000 bp<br>
bins, here is the command you would use:<br>
<a href="http://bp_generate_histogram.pl" target="_blank">bp_generate_histogram.pl</a>
-merge -d dicty -bin 10000 SNP<br>
>snp_density.gff<br>
This is saying to use the "dicty" database (-d) option, to use 10,000
bp<br>
bins (the -bin option) and to count the occurrences of the SNP feature<br>
throughout the database. In addition, the -merge option says to merge<br>
all types of SNPs into a single bin. Otherwise they will be stratified<br>
by their source. The resulting GFF file contains a series of entries<br>
like these ones:<br>
Chr1 SNP bin 1 10000 49 + . bin Chr1:SNP<br>
Chr1 SNP bin 10001 20000 29 + . bin Chr1:SNP<br>
What this is saying is that there are now a series of pseudo-features of<br>
type "bin:SNP" that occupy successive 10,000 bp regions of the
genome.<br>
The score field contains the number of times a SNP was seen in that bin.<br>
You'll now load this file using <a href="http://bp_load_gff.pl" target="_blank">bp_load_gff.pl</a>
or <a href="http://bp_fast_load_gff.pl" target="_blank">bp_fast_load_gff.pl</a>:<br>
<a href="http://bp_load_gff.pl" target="_blank">bp_load_gff.pl</a> -d
dicty snp_density.gff<br>
The next step is to tell GBrowse how to use this information. You do<br>
this by creating a new aggregator for the SNP density information. Open<br>
the GBrowse configuration file and find the aggregators option. Add a<br>
new aggregator that looks like this:<br>
aggregators = snp_density{bin:SNP}<br>
This is declaring a new feature named "snp_density" that is composed
of<br>
subparts of type bin:SNP.<br>
The last step is to declare a track for the density information. You<br>
will use the "xyplot" glyph, which can draw a number of graphs,<br>
including histograms. To add the SNP density information as a static<br>
track in the overview, create a section like this one:<br>
[SNP:overview]<br>
feature = snp_density<br>
glyph = xyplot<br>
graph_type = boxes<br>
scale = right<br>
bgcolor = red<br>
fgcolor = red<br>
height = 20<br>
key = SNP Density<br>
This is declaring a new constant track in the overview named "SNP<br>
Density." The feature is "snp_density", corresponding to the
aggregator<br>
declared earlier. The glyph is "xyplot" using the graph type of
"boxes"<br>
to generate a column graph.<br>
To set up a track so that the histogram appears when the user zooms out<br>
beyond 100,000 bp but shows the detailed information at higher<br>
magnifications, generate two track sections like these:<br>
[SNPs]<br>
feature = snp<br>
glyph = triangle<br>
point = 1<br>
orient = N<br>
height = 6<br>
bgcolor = blue<br>
fgcolor = blue<br>
key = SNPs<br>
[SNPs:100000]<br>
feature = snp_density<br>
glyph = xyplot<br>
graph_type = boxes<br>
scale = right<br>
The first track section sets up the defaults for the SNP track. SNPs are<br>
represented as blue triangles pointing North. The second track<br>
declaration declares that when the user zooms out to over 100K base<br>
pairs, GBrowse should display the snp_density feature using the xyplot<br>
glyph.<br>
<br>
========================================================================<br>
=============================<br>
<br>
How different is this for gbrowse2?<br>
<br>
<br>
Pushkala<br>
<br>
------------------------------------------------------------------------------<br>
Download Intel&#174; Parallel Studio Eval<br>
Try the new software tools for yourself. Speed compiling, find bugs<br>
proactively, and fine-tune applications for parallel performance.<br>
See why Intel Parallel Studio got high marks during beta.<br>
<a href="http://p.sf.net/sfu/intel-sw-dev" target="_blank">http://p.sf.net/sfu/intel-sw-dev</a><br>
_______________________________________________<br>
Gmod-gbrowse mailing list<br>
<a href="mailto:Gmod-gbrowse@lists.sourceforge.net" target="_blank">Gmod-gbrowse@lists.sourceforge.net</a><br>
<a href="https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse"
target="_blank">https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse</a><o:p></o:p></p>
</div>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><br>
<br clear=all>
<br>
-- <br>
===> PLEASE KEEP RESPONSES ON THE LIST <===<br>
<a href="http://gmod.org/wiki/GMOD_Logo_Program" target="_blank">http://gmod.org/wiki/GMOD_Logo_Program</a><br>
<a href="http://gmod.org/wiki/GMOD_News" target="_blank">http://gmod.org/wiki/GMOD_News</a><br>
Was this helpful? <a href="http://gmod.org/wiki/Help_Desk_Feedback"
target="_blank">http://gmod.org/wiki/Help_Desk_Feedback</a><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<p class=MsoNormal><br>
<br clear=all>
<br>
-- <br>
Lincoln D. Stein<br>
Director, Informatics and Biocomputing Platform<br>
Ontario Institute for Cancer Research<br>
101 College St., Suite 800<br>
Toronto, ON, Canada M5G0A3<br>
416 673-8514<br>
Assistant: Renata Musa <<a href="mailto:Renata.Musa@oicr.on.ca">Renata.Musa@oicr.on.ca</a>><o:p></o:p></p>
</div>
</div>
</body>
</html>