UCSC Track Hub Troubleshooting

Question

[Maliha]

I am working on making a track hub for "bos frontalis" in UCSC Genome Browser. While making the track hub I am facing a problem in creating trackdb.txt file. This is a completely new genome sequence and the data has not been published in the NCBI yet (So no accession number is available). I was wondering if I can use the data from my local server/ftp sites. So I do not understand what should I put in the place of "bigdataURL". I'd be grateful if you can help me with this.

Answer 1

[Matthias Zepper]

Yes, using and displaying data from your own server is the whole point of UCSC Track hubs, so your approach is feasible.

The trackDB.txt file is indeed a bit fiddly. The value for bigDataUrl value needs to point to your actual data file for the track, e.g. in bigWig, bigBed, vcf or bam format, depending on the source data type.

Take a look at the Track Database Definition reference for allowed and recommended parameters. There is also a specific guide on AssemblyHubs (hubs like yours for which no reference genome exists in UCSC) and how to group tracks to improve usability.