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
