Good Morning Jay:
We need to get your hgTrackDb command to load your table. Manually trying
to load settings into a trackDb table is a quixotic task.
Here is an example:
Here is my .ra file:
$ cat local.ra
track bsNonCpGPos
shortLabel Non-CpG Region +ive
longLabel RMAPBS raw out of non-CpG region +ive strand
group x
priority 8
visibility dense
itemRgb on
type bed 9 .
yLineOnOff on
yLineMark 10
minLimit 10
maxLimit 10
Loading it into a test table:
$ hgTrackDb . hg19 trackDb_test $HOME/kent/src/hg/lib/trackDb.sql .
-raName=local.ra
The contents of that table: (the cat -A shows all characters
$ hgsql -N -e "select * from trackDb_test;" hg19 | cat
bsNonCpGPos Non-CpG Region +ive bed 9 . RMAPBS raw out of non-CpG
region +ive strand 1 8 0 0 0
127 127 127 00 0 x 1
group x\nitemRgb on\nlongLabel RMAPBS raw out
of non-CpG region +ive strand\nmaxLimit 10\nminLimit 10\npriority 8\nshortLabel
Non-CpG Region +ive\ntrack bsNonCpGPos\ntype bed 9
.\nvisibility dense\nyLineMark 10\nyLineOnOff on\n
Note, all the settings you wanted are in the settings string.
You should be able to construct a table like this.
The definitions of all the settings allowed are in the trackDb/README file.
You can find examples of the usage of the settings in the trackDb.ra files
in the source tree.
--Hiram
Jaysheel Bhavsar wrote:
> Hi Hiram,
> If I understand your email, and the README files correctly all
> trackDb_local.ra will do is keep my tracks in a diff table from that comes
> with the src file. Which is all well and good, but the problem that I am
> facing is that when I run hgTrackDb weather on trackDb_local.ra or on
> trackDb.ra (edited with my tracks). The resulting trackDb_local.tab or
> trackDb.tab does not have any reference of the settings for a give track. I
> have passed -settings argument to hgTrackDb, but result is the same, the last
> column in trackDb.tab or trackDb_local.tab is always empty.
>
> Can you send me an example of what can be in settings field of trackDb.
> Specifically I need settings for bedGraph where yLineMark is set to 10,
> yLineOnOff is on, vertical viewing range is from 0 to 100.
>
> some guess work I tried which has been unsuccessful so far are:
>
> - If settings field in trackDb starts with 'minLimit 0, maxLimit 100' I
> get an error "invalid double 0, maxLimit"
> - If settings field in trackDb starts with 'yLineMark 10, yLineOnOff',
> I see y=10 under track settings for a given track but on/off drop down is
> always off.
> - If settings field in trackDb starts with 'yLineOnOff, yLineMark 10'
> everything has default values, when viewing track settings.
>
> Jaysheel
>
> p.s: I do have 'mthy' entry in grp table.
>
> On Apr 12, 2010, at 1:02 PM, Hiram Clawson wrote:
>
>> Good Morning Jay:
>>
>> I would recommending backing out any changes you have made in the source tree
>> trackDb hierarchy. Restore your trackDb tables to be identical to our
>> download copies. There is a newly documented easier way to construct your
>> own tracks without working in our source tree. See also, in the source tree:
>> http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.trackDb
>>
>> Construct your own private trackDb_local.ra file somewhere convenient,
>> with the contents:
>>
>> track bsNonCpGPos
>> shortLabel Non-CpG Region +ive
>> longLabel RMAPBS raw out of non-CpG region +ive strand
>> group x
>> priority 8
>> visibility dense
>> itemRgb on
>> type bed 9 .
>>
>> Load that into your own private trackDb table called: trackDb_local
>> with the command:
>>
>> hgTrackDb . hg19 trackDb_local $HOME/kent/src/hg/lib/trackDb.sql
>>
>> Adjust that pathname to the file trackDb.sql to be correct for
>> your setup there.
>>
>> Then, in your cgi-bin/hg.conf file, alter the db.trackDb definition line to
>> read:
>>
>> db.trackDb=trackDb_local,trackDb
>>
>> This will use your special table trackDb_local in addition to the
>> normal one from the source tree.
>>
>> You have mthy as a group designation ? Have you constructed a special
>> grp entry for that ? You can do the same trick with the grp table as
>> mentioned
>> above with the trackDb table for your own local grp definitions.
>> Look into the comments in the hg.conf file for the grp line just
>> like this trackDb line. This keeps all of your local changes out of
>> the UCSC tables so database updates will not destroy your local work.
>>
>> --Hiram
>>
>> Jaysheel Bhavsar wrote:
>>> Hey guys,
>>> So it seems that make trackDb isn't working as expected or my syntax is
>>> incorrect. I have following in my trackDb.ra
>>> ------------------------------------------------------------------------------------
>>> track cpgMeth
>>> shortLabel CpG Methylation
>>> longLabel RMAPBS CpG Methylation Ratio
>>> group mthy
>>> priority 4
>>> visibility full
>>> color 102,51,0
>>> type bedGraph
>>> minLimit 0
>>> maxLimit 100
>>> yLineMark 10.0
>>> yLineOnOff on
>>> track ncpgpos
>>> shortLabel Non-CpG +ive
>>> longLabel RMAPBS Non-CpG region positive strand
>>> group mthy
>>> priority 6
>>> visibility dense
>>> type bed 9 .
>>> itemRgb on
>>> ------------------------------------------------------------------------------------
>>> after running
>>>> make alpha GENOMENAME DBNAME trackDb.sql
>>> I get trackDb.tab file but in this there is no reference for itemRgb,
>>> minLimit, maxLimit, yLineMark and yLineOnOff. Shooting in the dark, I
>>> added 'itemRgb on' in trackDb.settings field and it worked, but I can't
>>> seem to get the settings for bedGraph. My max graphing bound is always
>>> 1000. Help...
>>> Thanks
>>> Jay
>
>
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