Hi Hiram,
It doesn't seem to work. I added itemRgb on in trackDb.ra but it
didn't seem to work. Please find attached part of my bed file, corresponding
bed.tab file created by hgLoadBed and my trackDb.ra. Perhaps my syntax is
incorrect.
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 .
On Apr 8, 2010, at 5:44 PM, Hiram Clawson wrote:
> It will work OK Jay. That is merely an older name for
> that column. It will function as RGB if you turn on that
> option in your trackDb_local.
>
> --Hiram
>
> ----- Original Message -----
> From: "Jaysheel Bhavsar" <[email protected]>
> To: [email protected]
> Sent: Thursday, April 8, 2010 2:35:00 PM GMT -08:00 Tijuana / Baja California
> Subject: [Genome] create bed file with itemRGB
>
> Hi guys,
> I want to create a track such that if there is any methylation in CpG
> motif they are colored differently from non methylated regions. Using
> Example 5 here
>
> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TRACK
>
> I though if I format my bed file properly ie.
> chr_1 start stop score name strand start stop rgb
>
> I would achieve the result, but that is not the case.
>
> After creating a bed file, I used hgLoadBed to load it into db. The table
> created has following fields
>
> bin | chrom | chromStart | chromEnd | name | score | strand | thickStart |
> thickEnd | reserved
>
> I was expecting the last field to be itemRGB, and not reserved. It seems
> that I am missing something here, did I not create the bed file correctly?
>
> Thank you
> Jay
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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