Adding custom tracks from URL in Arabidopsis thaliana

[Rafael Riudavets Puig]

Dear member of the UCSC Genome Browser team,

We have recently been trying to load custom tracks from BED file URLs in the UCSC genome browser. We have managed to do so for most of our data, but we finding some issues for files corresponding to Arabidopsis thaliana. An example URL of one of our files would be:

http://genome.ucsc.edu/cgi-bin/hgTracks?pix=1000&db=araTha1&hgt.customText=https://unibind.uio.no/static/data/20201216/macs/DAMO/EXP041453.3_day_old_seedlings.ABF1/EXP041453.3_day_old_seedlings.ABF1.MA0570.2.damo.bed

As you can see, we use db=araTha1. However, we saw that araTha1 is not listed in the UCSC codes here. Is there any way to load a BED file from a URL as a custom track in one of the available assembly hubs?

Thank you very much in advance for your help.

Best regards,

Rafael Riudavets Puig

[Hiram Clawson]

Good Morning Rafael:

Please try this URL to load your custom track on the A. thaliana assembly hub:


https://genome.ucsc.edu/h/GCF_000001735.4?hgt.customText=https://unibind.uio.no/static/data/20201216/macs/DAMO/EXP041453.3_day_old_seedlings.ABF1/EXP041453.3_day_old_seedlings.ABF1.MA0570.2.damo.bed

Note: Your chromosome names will change to RefSeq accession identifiers.
Check the sequences display to see the name equivalence after the assembly
hub is attached:

https://genome.ucsc.edu/cgi-bin/hgTracks?chromInfoPage=1

--Hiram

On 3/24/21 2:22 AM, Rafael Riudavets Puig wrote:
> Dear member of the UCSC Genome Browser team,
>
>
> We have recently been trying to load custom tracks from BED file URLs in the UCSC genome browser. We have managed to do so for most of our data, but we finding some issues for files corresponding to Arabidopsis thaliana. An example URL of one of our files would be:
>
> http://genome.ucsc.edu/cgi-bin/hgTracks?pix=1000&db=araTha1&hgt.customText=https://unibind.uio.no/static/data/20201216/macs/DAMO/EXP041453.3_day_old_seedlings.ABF1/EXP041453.3_day_old_seedlings.ABF1.MA0570.2.damo.bed
>
>

> As you can see, we use db=araTha1. However, we saw that araTha1 is not listed in the UCSC codes here<https://genome.ucsc.edu/FAQ/FAQreleases.html#release1>. Is there any way to load a BED file from a URL as a custom track in one of the available assembly hubs?