Good Afternoon Mo:
You can make a track like this function just fine if you
use the bigBed format instead of the GFF file format.
If you have access to a linux/unix work-station, I have included
below the commands you would use to convert your data to bigBed
and how it would be used in a custom track.
--Hiram
----- Original Message -----
From: "Mo Lee"
Cc: "Gary Stormo"
Sent: Thursday, July 21, 2011 12:35:27 PM
Subject: [Genome] Mo Lee from Washington University in St. Louis: C.elegans
regulatory sites (PhyloNet)
Hi!
I'd like to share my annotation track with a broader audience.
URL of my track:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=ce6&position=chrIV:17,471,786-17,493,785&hgt.customText=http://ural.wustl.edu/~molee0805/PhyloNet_sites.txt
We used GFF file format
Description: It is a collection of regulatory sites of C.elegans generated
by a program we developed in the lab called PhyloNet.
I have been trying to upload the URLs, both
http://ural.wustl.edu/~molee0805/PhyloNet_sites.txt<http://genome.ucsc.edu/cgi-bin/hgTracks?db=ce6&position=chrIV:17,471,786-17,493,785&hgt.customText=http://ural.wustl.edu/%7Emolee0805/PhyloNet_sites.txt>,
which is GFF file itself on our website and
http://ural.wustl.edu/~molee0805/homepage.html, which is a website that
contains information of each site in detail( Additional annotation website
for our data). Each time I uploaded them, it worked fine on the same age I
uploaded. However, when I wanted to click on the link in a new window after
I closed the original one, it takes a long time to load our custom track and
the extra link which contains the detailed information of each site is never
there in the description box below the general information that comes from
UCSC browser when you click on a specific site in the custom track.
Hopefully, you can help us with it because I have tried many ways, and it
never really works.
Thank you very much!!
Mo
== Commands to construct and use a bigBed format file =====
# eliminate the track line from your gff file
grep "^chr" PhyloNet_sites.txt > phyloNetSites.gff
# eliminate the duplicate rows from your gff file,
# convert the data to a .bed file sorted by chromosome and start position
sort -u phyloNetSites.gff \
| awk '{printf "%s\t%d\t%d\t%s\t0\t%s\n", $1, $4-1, $5, $9, $7}' \
| sort -k1,1 -k2,2n > phyloNetSites.bed
# obtain kent source commands from UCSC FTP server
# If linux.x86_64 is not your machine type (see output of command: uname -a)
# check the other possible machine types at:
# ftp://hgdownload.cse.ucsc.edu/apache/htdocs/admin/exe/
wget --timestamping \
ftp://hgdownload.cse.ucsc.edu/apache/htdocs/admin/exe/linux.x86_64/fetchChromSizes
wget --timestamping \
ftp://hgdownload.cse.ucsc.edu/apache/htdocs/admin/exe/linux.x86_64/bedToBigBed
wget --timestamping \
ftp://hgdownload.cse.ucsc.edu/apache/htdocs/admin/exe/linux.x86_64/bigBedSummary
wget --timestamping \
ftp://hgdownload.cse.ucsc.edu/apache/htdocs/admin/exe/linux.x86_64/bigBedInfo
chmod +x fetchChromSizes bedToBigBed bigBedSummary bigBedInfo
# obtain ce6 chrom sizes from UCSC
./fetchChromSizes ce6 > ce6.chrom.sizes
# convert your .bed file to a bigBed file:
./bedToBigBed phyloNetSites.bed ce6.chrom.sizes phyloNetSites.bb
# verify the bigBed file is legitimate
./bigBedInfo phyloNetSites.bb
Place the phyloNetSites.bb file on a WEB server at a URL,
use that URL in the bigDataUrl specification on a single track
line for your custom track:
http://genome.ucsc.edu/goldenPath/help/bigBed.html
For example, you can use the URL you indicated:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=ce6&position=chrIV:17,471,786-17,493,785&hgt.customText=http://ural.wustl.edu/~molee0805/PhyloNet_sites.txt
But in this case, your PhyloNet_sites.txt file instead of containing
the GFF data, has a single track line (all of this must be on a
single line):
track type=bigBed name=PhyloNet Sites
description="regulatory elements of C.elegans"
bigDataUrl="http://ural.wustl.edu/~molee0805/phyloNetSites.bb";
url="http://ural.wustl.edu/~molee0805/Motif/$$.html";
If you can construct your names to correspond to the function
of your website, the "$$.html" in the url specification will allow
clicks directly from the genome browser to your data site.
The $$ becomes a substitution of the name column from your bed file.
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