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
>
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