You can also investigate your track data with the "tables" browser function. Select your track, full genome region, and ask for a "statistics" display. That will either show you all your data, or indicate some error. Check your Apache error logs for errors as you work with your track.
--Hiram Hiram Clawson wrote: > 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
