Thanks Brooke, I will see if changing the names make a difference.
Jay
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
_______________________________________________
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