User talk:Fubar

Things worth remembering that might be useful for other UCSC mirror builders

Notes

Galaxy notes: Fubar:GalaxyNotes

Some random notes on installing a mirror under CentOS: CentOS_notes

Some notes on adding a custom track: Custom_track

Code of potential use for mirror sites

The ucsc wiki can't set a cookie for your local mirror, so here's an example of LDAP authentication for local mirrors: Fubar:LDAP_auth

Gripes

Wiggle tracks need a bar graph option - points or joined points can be very misleading! Ah, bedGraph mentioned in ..kent/src/hg/makeDb/trackDb/README does the trick. It's an ordinary 9 column bed file with extra options including bars which are much more appropriate for (eg) -log10(p) values from an analysis eg. I am making custom tracks using (eg)

 
track bdrabpctmincov
priority 2.100
shortLabel bdrabpctmincov
longLabel CAMP 2007 pbat additive model -log10(p) bdrabpctmincov  
visibility hide
type bedGraph
autoScale off
viewLimits 0:7
minLimit 0
maxLimit 7
maxHeightPixels 60:40:40
color 56,88,9
group phenDis

Solutions

I think you may be confusing "wiggle tracks" here with the "chromGraph" tracks in the "Genome Graphs" function of the browser. Wiggle tracks are by default bar graphs. The width of the bar in one of these graphs is the "span" of the data. Each specified data point applies to "span" number of bases. See also, the discussion about the proper usage of "span" in Wiggle_BED_to_variableStep_format_conversion.

On the other hand, the "Genome Graphs" "chromGraph" data is completely different than wiggle tracks. In the chromGraph format, each specified data point is merely a point and has no defined span to apply to a number of bases. In this graph, each point is simply connected to the next point with a line. It is a line graph, not a bar graph. The chromGraph data does not have the ability to define how large to make bars for a bar graph. Certainly something to think about for future improvements, but the purpose of chromGraph data is different than wiggle tracks.

Also, your note about mentions the bedGraph wiggle format. Please note the discussion of the drawbacks of the bedGraph wiggle format in the above mentioned link: Wiggle_BED_to_variableStep_format_conversion

Hiram 09:12, 2 July 2007 (PDT)