Question: a webserver for the bigwig files
1
gravatar for Bogdan
12 weeks ago by
Bogdan750
Palo Alto, CA, USA
Bogdan750 wrote:

Dear all, would you please advise :

which (public) webserver would you recommend to host the bigwig files, in order to upload the tracks in the UCSC browser ?

thank you very much,

-- bogdan

bigwig • 213 views
ADD COMMENTlink modified 11 weeks ago • written 12 weeks ago by Bogdan750

You could set something up in the cloud yourself, if you have access to necessary funds. Otherwise there are likely not many (or any?) public options (because of size of data sets and security concerns).

ADD REPLYlink written 12 weeks ago by genomax67k

yes, thank you, what cloud service would you recommend ?

ADD REPLYlink written 12 weeks ago by Bogdan750

Google compute, AWS, Azure would all work. Google compute seems to be more user friendly. You can sign up for a free trial ( they offer like $300 compute credits) to see if it would work for your purposes. There is all sorts of online help available. You can easily set a public webserver up with local storage.

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by genomax67k

thanks, yes, a Google Cloud bucket will help. Just came across a description on ENCODE page : https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/docs/tutorial_google.md

ADD REPLYlink written 12 weeks ago by Bogdan750
1
gravatar for max
12 weeks ago by
max20
max20 wrote:

See the UCSC docs https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html#Hosting

One free option, at reduced speed, is Cyverse. Two other free options, with higher speed but limited file sizes, are Figshare and Github.

As for the paid options, the UCSC page says this:


In general, commercial online cloud backup providers that charge a flat rate, like Dropbox, iCloud, Google Drive, Box.com, Microsoft OneDrive, Tencent Weiyun, Yandex.Disk, etc. do not work reliably as their business model requires rare and rate-limited data access, which is too slow or too limited for genome annotation display. However, commercial cloud storage offers that charge per GB transferred, like Amazon S3, Microsoft Azure Storage, Google Cloud Storage, Backblaze, Alibaba Object Store, etc. typically do work. For optimal performance, select a San Francisco / San Jose data center for the main UCSC site genome.ucsc.edu, a Frankfurt/Germany data center for genome-euro.ucsc.edu and a Tokyo data center for genome-asia.ucsc.edu.


Also, you can send email to the public mailing list at UCSC and ask us, as you did here.

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by max20
0
gravatar for Bogdan
11 weeks ago by
Bogdan750
Palo Alto, CA, USA
Bogdan750 wrote:

Thank you. Yes, the answer from UCSC folks was :

"There are a few different public options you can use to host your big* data. A number of our users utilize CyVerse (http://www.cyverse.org/), but I encourage you to look at our FAQ page on the topic and explore all the options (https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html#Hosting).

Another option is to run a local copy of the Genome Browser on a virtual machine, which allows you to view big* files directly from your computer. If this seems like a valid solution, I would recommend you look at our GBiB documentation (https://genome.ucsc.edu/goldenpath/help/gbib.html#What). There is a specific section on that page that covers viewing your own data on the GBiB including big* files (https://genome.ucsc.edu/goldenpath/help/gbib.html#YourTracks)."

ADD COMMENTlink written 11 weeks ago by Bogdan750
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