How To Load Multiple Bed Files To Ucsc Genome Browser By Url And With Track Annotation

Question

[Tky]

I am trying to view several bed files in UCSC genome browser. Since the size is larger than 500 Mb, which exceeds the upload limit of UCSC,

I put the files to dropbox and paste the URLs to UCSC and it works without problem.

However all files contains no header line information, I could not paste multiple files to UCSC.

I am wondering whether there is a way to supply the track name and description with each URL. I have tried as shown below but without success,

track name='track1' description='tack information' URL=https://dl.dropboxusercontent.com/u/189277187/1-2.fq.sorted.bed

I hope you can point out a solution, with many thanks in advance,

Answer 1

[David Langenberger]

You can try to use Track Hubs. Should work for your problem. It's a bit tricky to get them working, but UCSC provides a step-by-step instruction.

[Tky]

Thanks for pointing out the Track hubs! Unfortunately bed file is not supported. I guess I have to convert to bigbed files.

[David Langenberger]

Ah ok, try Galaxy, it has a bed2bigbed converter.

Answer 2

[Vikas Bansal]

I think you have to convert your bed file to BigBed. You can use bedtoBigBed from UCSC. E.g.

bedToBigBed   sorted.bed    mm9.chrlist    sorted.bb

Then you can just upload your BigBed online (which have third party access permissions) and you can paste the below code in UCSC -

##choose mm9 assembly
browser hide all
browser pack refGene

track name=Example db=mm9 type=bigBed visibility=4 bigDataUrl=https://your_URL/sorted.bb

Please change reference genome accordingly.

[Tky]

hi, Vikas, thanks for the help. so basically it is not possible to feed UCSC bed files with track name? The files are located in a windows computer and I do not have the linux enviroment at this moment, I would prefer a way to directly use bed files.

[Vikas Bansal]

I am not sure if we can use bed files directly in this way. I tried it in the past, it was not possible.