forget the link. http://research.icts.uiowa.edu/genomebrowser/cgi-bin/hgTrackUi?hgsid=27&c=chrX&g=wigExample
On Fri, May 7, 2010 at 12:02 AM, Tiandao Li <[email protected]> wrote: > Hi Hiram, > > I looked through README files several times, src/product/README.trackDb and > src/hg/makeDb/trackDb/README. > > I loaded my original wig file to UCSC genome browser to ensure the > data/format is right. > > The next are the commands I used to load tracks to local browser. > > [l...@research tmp]$ /opt/kent/wigEncode PolII_eland_sorted2.wig PolII.wig > PolII.wib > > Converted PolII_eland_sorted2.wig, upper limit 4385.00, lower limit 2.00 > > [l...@research ~]$ /opt/kent/hgLoadWiggle hg18 wigExample PolII.wig > > Connected to database hg18 for track wigExample > Creating wiggle table definition in hg18.wigExample > Saving wiggle.tab > WARNING: Exceeded chrM size 16624 > 16571. dropping 3 data point(s) > Loading hg18 > > [l...@research tmp]$ cp PolII.wib /gbdb/hg18/wib/ > I don't know the above is needed or not, but I follow the help of > wigEncode. > > [l...@research tmp]$ /opt/kent/hgTrackDb human hg18 trackDb_wigExample > ~/bin/kent/src/hg/lib/trackDb.sql . > > Loaded 1 track descriptions total > Loaded database hg18 > [l...@research tmp]$ /opt/kent/hgFindSpec human hg18 hgFindspec_wigExample > ~/bin/kent/src/hg/lib/hgFindSpec.sql . > > Loaded 0 search specs total > Loaded database hg18 > > also edit hg.conf file, > > vim /var/www/html/genomebrowser/cgi-bin/hg.conf > db.trackDb=trackDb,trackDb_wigExample > > Please check the following link, looks like the data and track > specifications in database, however, there isn't any bars on the website. > > Thanks, > > Tiandao > > > [l...@research tmp]$ more trackDb.ra > track wigExample > > shortLabel Pol II > longLabel Pol II in 25-Base Windows > group user > priority 23.5 > visibility full > autoScale On > > maxHeightPixels 128:36:16 > graphTypeDefault Bar > gridDefault OFF > windowingFunction Mean > color 0,0,0 > altColor 128,128,128 > viewLimits 30:70 > spanList 5 > type wig 0 100 > [l...@research tmp]$ > > mysql> select * from trackDb_wigExample; > > +------------+------------+-----------+---------------------------+------------+----------+--------+--------+--------+-----------+-----------+-----------+----------+---------+---------------+--------------+-----+------+------+---------+---------------------------------------------------------------------------------------------------------------------------------+ > | tableName | shortLabel | type | longLabel | > visibility | priority | colorR | colorG | colorB | altColorR | altColorG | > altColorB | useScore | private | restrictCount | restrictList | url | html | > grp | canPack | > settings > | > > +------------+------------+-----------+---------------------------+------------+----------+--------+--------+--------+-----------+-----------+-----------+----------+---------+---------------+--------------+-----+------+------+---------+---------------------------------------------------------------------------------------------------------------------------------+ > | wigExample | Pol II | wig 0 100 | Pol II in 25-Base Windows > | 2 | 23.5 | 0 | 0 | 0 | 128 | 128 > | 128 | 0 | 0 | 0 | | | > | user | 0 | autoScale On > > graphTypeDefault Bar > gridDefault OFF > maxHeightPixels 128:36:16 > spanList 5 > viewLimits 30:70 > windowingFunction Mean > | > > +------------+------------+-----------+---------------------------+------------+----------+--------+--------+--------+-----------+-----------+-----------+----------+---------+---------------+--------------+-----+------+------+---------+---------------------------------------------------------------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > > > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
