Question: error in uploading bigbed file on UCSC
0
gravatar for ashkan
3.3 years ago by
ashkan110
ashkan110 wrote:

I made bigbed files from my bed files and I am trying to upload it to the UCSC. but it gives this error:

"Error File '2_accepted_hits.bb' - It appears that you are directly uploading binary data of type bigBed. Custom tracks of this type require the files to be accessible by public http/https/ftp, and file URLs must be passed as the bigDataUrl setting on a "track" line."

I also have uploaded it to dropbox. so, I also give the link like this: "track type=bigBed name="My Big Bed" description="A Graph of Data from My Lab" bigDataUrl=http://myorg.edu/mylab/myBigBed.bb". but it gives this error: " Error No Content-Length: returned in header for https://www.dropbox.com/home?preview=2_accepted_hits.bb, can't proceed, sorry"

then I tried to give link and upload the file. but did not work!

do you guys know how to solve this problem?

ucsc rna-seq sequencing • 1.4k views
ADD COMMENTlink modified 3.3 years ago by Emily_Ensembl19k • written 3.3 years ago by ashkan110
1

Drop box and similar sites tend to not easily provide direct links to only the file. Assuming you're at a university, upload it to some public server there.

Better yet, use IGV or a another local browser.

ADD REPLYlink written 3.3 years ago by Devon Ryan91k

Once your files are on a public server (as suggested by @Devon Ryan) (btw, could you submit them to The Track Hub Registry?) you could try attaching them to the Ensembl genome browser, if your species is in there. Check the tutorial page on Use my own data in Ensembl.

ADD REPLYlink written 3.3 years ago by Denise - Open Targets5.0k

@Denise: This continues to a vexing problem for many users. Security considerations have eliminated large public web accessible locations at many institutions and it is beyond the scope of individuals to manage web servers/personal spaces.

Perhaps @Ensembl should offer a service where users can upload such files (after some kind of authentication/validation of the users via an account). You could limit the amount of time files can stay at this location to avoid storage problems.

ADD REPLYlink written 3.3 years ago by genomax71k

@genomax2, not sure if I understand your suggestion here. One can already register and have an Ensembl account, which is free. Login to Ensembl and upload (or attach) BigBED (or other) files. For files larger than 20MB, the data needs to be on a server, and attached as a http, https, ftp. When logged in, the files will be kept in the user's account for as long as Ensembl is up and running (hopefully for at least another 16 years to come). If not logged in, the files will be kept in the server for a month or so. Ensembl account holders won't get any emails from the team. If @behzadmoumbeini's file is smaller than 20MB, uploading the data onto Ensembl should not be a problem.

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Denise - Open Targets5.0k

File size problem is what I was specifically referring to. 20MB is not going to cut it for many NGS related files people are trying to project against Ensembl annotation and not everyone can get access to a web location to put the files up for http/ftp access.

My line of thought was that if Ensembl is able to validate a user as belonging to a known institution (e.g. University etc) Ensembl could allow users to upload files that can be much larger than 20MB. An ftp mechanism like what Galaxy uses could technically be used. Large files can be made to expire as soon as the user closes the current session (or within 24h or so).

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by genomax71k

Someone else had recently commented here that dropbox no longer appears to allow unrestricted access to inbound http(s) connections so this option no longer works for UCSC browser.

Unless you have a specific reason you should try a local browser like @Devon suggested below. Other option would be to make separate files per chromosomes and see if you can get around the upload size limit.

ADD REPLYlink written 3.3 years ago by genomax71k
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