Getting genome and annotation information from custom UCSC genome browser

[Manoj Kandpal]

Dear UCSC genome browser team,

Thank you so much for crating such a wonderful tool. 

I am following an article which has uses a  custom UCSC browser at, http://vader.wistar.upenn.edu/. Is it possible to get the whole genome fasta and gtf for this particular custom browser, humanSTF500?

I could get the fasta from their original publication (https://genome.cshlp.org/content/24/6/1039.full) but it does not completely matched with this updated one.

I tried the browser table but can’t get the data of interest, genome seq (fa) and annotation (gtf) file. 

http://vader.wistar.upenn.edu/cgi-bin/hgTables?hgsid=8699_u1cbEeOw3BOrJaH9aAMfmqLQQwEp&hgSeq.promoter=on&boolshad.hgSeq.promoter=0&hgSeq.promoterSize=1000&hgSeq.utrExon5=on&boolshad.hgSeq.utrExon5=0&hgSeq.cdsExon=on&boolshad.hgSeq.cdsExon=0&hgSeq.utrExon3=on&boolshad.hgSeq.utrExon3=0&hgSeq.intron=on&boolshad.hgSeq.intron=0&hgSeq.downstream=on&boolshad.hgSeq.downstream=0&hgSeq.downstreamSize=1000&hgSeq.granularity=feature&hgSeq.padding5=0&hgSeq.padding3=0&boolshad.hgSeq.splitCDSUTR=0&hgSeq.casing=upper&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=N&hgta_doMainPage=cancel

I would really appreciate any help.

regards,

Manoj Kandpal, Ph.D., M.Tech.

Research Assistant Professor

Department of Preventive Medicine – HBMI

Northwestern University - Feinberg School of Medicine

750 N Lake Shore Drive, 11-150

Chicago, IL, USA 60611

Tel: 1-312-503-2310

[Hiram Clawson]

Good Morning Dr. Kandpal:

You would need to write to the authors of the paper to see if they
have the sequences available. The browser you mention is not configured
for the downloads of the sequence data and associated annotations.

--Hiram Clawson

U.C. Santa Cruz Genomics Institute

> Department of Preventive Medicine - HBMI