Thank you for your reply.

Trying to pass blockSizes as a column with i.e. "20,20", disrupts the
interaction with UCSC. My RangedData looks like this.

RangedData with 24 rows and 9 value columns across 1 space
         space             ranges |     itemRgb     score        name
thickStart  thickEnd blockCount  blockSizes blockStarts   strand
   <character>          <IRanges> | <character> <numeric> <character>
<numeric> <numeric>  <numeric> <character> <character> <factor>
1         chr2 [5971505, 5972574] |       0,0,0      1000
Upf2          0         0          2       20,20      0,1049        +
2         chr2 [5872579, 5878536] |       0,0,0      1000
Upf2          0         0          2       20,20      0,5937        +
3         chr2 [5872579, 5955177] |     150,0,0      1000
Upf2          0         0          2       20,20     0,82578        +
4         chr2 [5950571, 5955177] |       0,0,0      1000
Upf2          0         0          2       20,20      0,4586        +
5         chr2 [5872579, 5894534] |     150,0,0      1000
Upf2          0         0          2       20,20     0,21935        +
6         chr2 [5882738, 5894534] |       0,0,0      1000
Upf2          0         0          2       20,20     0,11776        +
7         chr2 [5948514, 5950427] |       0,0,0      1000
Upf2          0         0          2       20,20      0,1893        +
8         chr2 [5947344, 5948278] |       0,0,0      1000
Upf2          0         0          2       20,20       0,914        +
9         chr2 [5961587, 5967963] |       0,0,0      1000
Upf2          0         0          2       20,20      0,6356        +
10        chr2 [5909498, 5924610] |       0,0,0      1000
Upf2          0         0          2       20,20     0,15092        +

Removing bockSizes and blockStarts from the object allows upload, but of
course doesn't get me what I need. Furthermore, how do I enable colors as
per the preamble itemRgb=On in custom tracks?

Thank you in advance,

Johannes

On Mon, Nov 23, 2009 at 3:31 PM, Michael Lawrence <mflawren@fhcrc.org>wrote:

>
>
> On Mon, Nov 23, 2009 at 2:08 AM, Johannes Waage <johannes.waage@gmail.com>wrote:
>
>> Hi all,
>>
>> Rtracklayer interacts nicely with UCSC GB, but does anyone know if there
>> is
>> support for uploading and displaying BED-tracks with thin and thick lines
>> (e.g. for visualizing splice-junction data from RNA-seq).
>> Is it possible to manipulate thickStart and thickEnd as well as other
>> optional BED-fields?
>>
>>
> All BED fields are supported. If your RangedData has the thickStart and
> thickEnd columns, they will be transmitted to the browser, as long as you're
> using the BED format for the transmission. By default, the format is
> automatically determined. Basically, BED is only used when there is no
> numeric score column, otherwise WIG or bedGraph is chosen. To force BED,
> pass format = "bed" when uploading the track.
>
>
>> Thanks in advance,
>>
>> JW,
>> Biotech Researh and Innovation Center
>> Uni. of Copenhagen
>>
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>>
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>
>

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