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
On Apr 9, 2010, at 4:37 PM, Brooke Rhead wrote:
> Hi Jay,
>
> The track info for fox2ClipSeq is in the kent source at
> src/hg/makeDb/trackDb/human/trackDb.ra, line 3128:
>
> track fox2ClipSeq
> subTrack fox2ClipSeqCompViewreads
> shortLabel FOX2 CLIP-seq
> longLabel FOX2 adaptor-trimmed CLIP-seq reads
> subGroups view=reads
> priority 1
> type bed 9 .
> itemRgb on
> noInherit on
> noScoreFilter .
>
> --
> Brooke Rhead
> UCSC Genome Bioinformatics Group
>
> On 04/09/10 13:06, Jaysheel Bhavsar wrote:
>> Hi Brooke,
>> What does your track info look like? Does your track in DB have any
>> mention of itemRgb? Jaysheel
>> On Apr 9, 2010, at 3:32 PM, Brooke Rhead wrote:
>>> Hello Jay,
>>>
>>> As Hiram mentioned, the rgb values being converted into a number and saved
>>> in a field called "reserved" is just an older convention -- it should still
>>> function correctly. An example table in our hg18 database with the exact
>>> same behavior is fox2ClipSeq ("FOX2 CLIP-seq" in the regulation section):
>>>
>>>> $ hgsql -e "select * from fox2ClipSeq limit 1" hg18
>>>> +-----+-------+------------+----------+--------------+-------+--------+------------+----------+----------+
>>>> | bin | chrom | chromStart | chromEnd | name | score | strand |
>>>> thickStart | thickEnd | reserved |
>>>> +-----+-------+------------+----------+--------------+-------+--------+------------+----------+----------+
>>>> | 585 | chr1 | 6088 | 6122 | ES_8_1941715 | 1 | - |
>>>> 6088 | 6122 | 16711680 |
>>>> +-----+-------+------------+----------+--------------+-------+--------+------------+----------+----------+
>>> This track functions normally in the browser, with items displayed in blue
>>> and red.
>>>
>>> Your syntax looks right. I was able to load your table and see all items
>>> displayed in blue except for the last one, displayed in red. However, I had
>>> to change your chrom names from "chr_1" to "chr1". Are you using an
>>> assembly with chromosome names like "chr_1"? If not, perhaps that is the
>>> problem.
>>>
>>> --
>>> Brooke Rhead
>>> UCSC Genome Bioinformatics Group
>>>
>>>
>>>
>>> On 04/09/10 11:17, Jaysheel Bhavsar wrote:
>>>> Hi guys,
>>>> Any idea how I can get itemRgb working. Attached is part of by bed
>>> file, bed.tab and trackDb.ra. After I run hgLoadBed, by rbg values get
>>> converted into some number and are saved in db in a field called
>>> "reserved", and after running make to create trackDb.tab I don't see any
>>> reference of itemRgb in trackDb.tab.
>>>>
>>>> Perhaps my syntax is incorrect? Help!!!!!!! Jay
>>>> nonCpG.pos.strand.out:
>>>> ----------------------------------------------------------
>>>> chr_1 7344 7345 C:1 0 + 7344 7345 51,51,153
>>>> chr_1 7346 7347 C:1 0 + 7346 7347 51,51,153
>>>> chr_1 7348 7349 C:1 0 + 7348 7349 51,51,153
>>>> chr_1 7357 7358 C:1 0 + 7357 7358 51,51,153
>>>> chr_1 7358 7359 C:1 0 + 7358 7359 51,51,153
>>>> chr_1 7361 7362 C:2 0 + 7361 7362 51,51,153
>>>> chr_1 7371 7372 C:6 0 + 7371 7372 51,51,153
>>>> chr_1 7376 7377 C:6 17 + 7376 7377 255,102,51
>>>> bed.tab: (created by hgLoadBed)
>>>> ----------------------------------------------------------
>>>> 585 chr_1 7344 7345 C:1 0 + 7344 7345
>>>> 3355545
>>>> 585 chr_1 7346 7347 C:1 0 + 7346 7347
>>>> 3355545
>>>> 585 chr_1 7348 7349 C:1 0 + 7348 7349
>>>> 3355545
>>>> 585 chr_1 7357 7358 C:1 0 + 7357 7358
>>>> 3355545
>>>> 585 chr_1 7358 7359 C:1 0 + 7358 7359
>>>> 3355545
>>>> 585 chr_1 7361 7362 C:2 0 + 7361 7362
>>>> 3355545
>>>> 585 chr_1 7371 7372 C:6 0 + 7371 7372
>>>> 3355545
>>>> 585 chr_1 7376 7377 C:6 17 + 7376 7377
>>>> 16737843
>>>> trackDb.ra entry:
>>>> ----------------------------------------------------------
>>>> track bsNonCpGPos
>>>> shortLabel Non-CpG Region +ive
>>>> longLabel RMAPBS raw out of non-CpG region +ive strand
>>>> group mthy
>>>> priority 8
>>>> visibility dense
>>>> itemRgb on
>>>> type bed 9 . _______________________________________________
>>>> Genome maillist - [email protected]
>>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
