Click through to your track user interface and look at what numbers are displayed for the limits of what you can display.
--Hiram WANG Wuqi wrote: > Hi Hiram, > > I ever tried to put "type 1.0 2413.0" in trackDb.ra, but still same > problems. > > Could you try to load this data in your side to see whether ok? > > > Thanks & Regards > > Wuqi > > > > -----Original Message----- > From: Hiram Clawson [mailto:[email protected]] > Sent: Friday, June 26, 2009 2:26 PM > To: WANG Wuqi > Cc: [email protected] > Subject: Re: [Genome] Load Wiggle Error > > > As I mentioned before, you need to put your minimum and maximum values > of your data on your 'type wig' line. Look at the trackDb/README file > for examples, and in many of the existing trackDb.ra files. > > --Hiram > > WANG Wuqi wrote: >> Hi Jennifer Jackson, >> >> Answer below: >> >> When you say compile track, do you mean that you ran "make" from the >> directory kent/src/hg/makeDb/trackDb ? >> >>>>>> Yes, command is "make alpha DBS=hg18" in above directory >> Some simple things to check. I am assuming that you used an existing >> track and copied that trackDb.ra file data to create your own. >> 1) What "group" was the track assigned to? This is where to look. You >> may want to make up your own group for your own local data. >> >>>>>> our own group 'gistrack', there are many tracks in this group >> >> 2) Is the track set as visible? -- trackDb.visibility >> 3) Did you add the data to to the top level for the organism or down >> in >> the particular assembly's trackDb.ra file? Are there any >> tableName/shortLabel/longLable conflicts? >> >> data in trackDb.ra: >> ------------------- >> track chr2_positive_strand >> shortLabel chr2_positive_strand >> longLabel chr2_positive_strand >> group gistrack >> priority 58 >> visibility hide >> color 175,150,128 >> altColor 255,128,0 >> type wig >> ------------------- >> 4) Did you create an html track description? >> >>>>>> No >> >> If you want to send in the section of your trackDb.ra file with the >> track's data (to just Hiram and me) we can look at it and provide >> feedback. Please also send the exact command you used to run "make" to > >> update the database, the path of the trackDb.ra file, and the cvs >> version of the trackDb.ra file that you started with. >>>>>> tracjDb.ra as attachment >>>>>> make alpha DBS=hg18 in >> /home/wangp/jksrc/kent/src/hg/makeDb/trackDb( >> this is our installation path). >> >>>>>> trackDb.ra path: >> /home/wangp/jksrc/kent/src/hg/makeDb/trackDb/human/hg18 >>>>>> it seems there is not version control for trackDb.ra >> By the way, we can add any other permanent trackpara in our group >> 'gistrack' And no any problems, but only this 2-columns wiggle can not > >> be seen. >> >> >> Thanks & Regards >> >> Wuqi >> >> >> -----Original Message----- >> From: Jennifer Jackson [mailto:[email protected]] >> Sent: Saturday, June 20, 2009 3:36 AM >> To: WANG Wuqi >> Cc: Hiram Clawson; [email protected] >> Subject: Re: [Genome] Load Wiggle Error >> >> >> Hello, >> >> When you say compile track, do you mean that you ran "make" from the >> directory kent/src/hg/makeDb/trackDb ? >> >> Some simple things to check. I am assuming that you used an existing >> track and copied that trackDb.ra file data to create your own. >> 1) What "group" was the track assigned to? This is where to look. You >> may want to make up your own group for your own local data. >> 2) Is the track set as visible? -- trackDb.visibility >> 3) Did you add the data to to the top level for the organism or down > in >> the particular assembly's trackDb.ra file? Are there any >> tableName/shortLabel/longLable conflicts? >> 4) Did you create an html track description? >> >> If you want to send in the section of your trackDb.ra file with the >> track's data (to just Hiram and me) we can look at it and provide >> feedback. Please also send the exact command you used to run "make" to > >> update the database, the path of the trackDb.ra file, and the cvs >> version of the trackDb.ra file that you started with. >> >> Jennifer Jackson >> UCSC Genome Bioinformatics Group >> >> WANG Wuqi wrote: >>> Hi Hiram, >>> >>> Sorry late for replying. >>> >>> This data can do custom track, no any problems. >>> >>> I want to do a permanent track for this data, and load data, add >>> entry >>> in trackDb.ra and compile track are ok, but we can not see this track >>> in genome browser. I can query this table from database and see many >>> rows, also there is this >>> track's info in table 'trackDb'. >>> >>> My problems is why this permanent track can not display in genome >>> browser? >>> >>> >>> Thanks & Regards >>> >>> Wuqi >>> >>> >>> >>> >>> -----Original Message----- >>> From: Hiram Clawson [mailto:[email protected]] >>> Sent: Thursday, June 11, 2009 1:16 AM >>> To: WANG Wuqi >>> Cc: [email protected]; OW Jack Ling; LEE Seow Eng >>> Subject: Re: Load Wiggle Error >>> >>> Your data is only on chr2, look at chr2 for your track. >>> >>> Look in your Apache error log to see if there are any >>> errors indicating what may be missing. >>> >>> Verify your custom track database configuration: >>> http://genomewiki.ucsc.edu/index.php/Using_custom_track_database >>> >>> --Hiram >>> >>> WANG Wuqi wrote: >>> >>>> Hi Hiram, >>>> >>>> The data of Wiggle format can be uploaded to our Genome browser >>>> mirror side and MySQL table has this data, no encounter any > problems. >>>> But the problem is that we can not see this track in Genome browser. >>>> >>>> Source data as attachment >>>> >>>> Please help >>>> >>>> >>>> Thanks & Regards >>>> >>>> Wuqi >>>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
