Question: Visualize bigwig, bedgraph, wig files on Genome Browser?
1
gravatar for salamandra
3 months ago by
salamandra130
salamandra130 wrote:

Hi,

I tried to visualize on genome browser a bigwig file that i created from a bam file (using the bamCoverage tool). When uploading the file it gives the error: "Error File 'something.bw' - It appears that you are directly uploading binary data of type bigWig. 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."

As sugested online I tried to upload to both googleDrive and dropbox and then provide the URL, but then it gave the errors: " Error Couldn't open https://www.dropbox.com/blablabla=0" " Error Unrecognized format line 1 of https://drive.google.com/blablabladrive_web:"

Then I tried with bedgraph (.bdg) format, but can only see the track as bars..it doesn't show peaks Already tried to convert from bigwig to wig and use the wig fie, but again can only see the track as bars, no peaks.

How to solve this? Please, help!

ADD COMMENTlink modified 3 months ago by Buffo1.1k • written 3 months ago by salamandra130

duplicate of : Visualizing bigwig files in UCSC genome browser ; Visualizing Chip-Seq Data Using Ucsc [Bigwig]

ADD REPLYlink written 3 months ago by Pierre Lindenbaum108k

well, the links you provided say "Now you have the bigwig file so lets upload it to ucsc. For that, just copy it on your local webserver, where you can get the link to the file like https://projects/files/file.bw". I don't have a server, does it mean I can't upload bigwig files to genomebrowser?

ADD REPLYlink written 3 months ago by salamandra130
3
gravatar for genomax
3 months ago by
genomax49k
United States
genomax49k wrote:

Take a look at this FAQ from UCSC and the section towards the end that talks about Cyverse. That may be your only option if you can't get your colleagues to set up a web accessible resource for you.

ADD COMMENTlink written 3 months ago by genomax49k

It worked! Thank you very much!

ADD REPLYlink written 3 months ago by salamandra130
0
gravatar for Buffo
3 months ago by
Buffo1.1k
Buffo1.1k wrote:

Try IGV browser, it works for me.

ADD COMMENTlink written 3 months ago by Buffo1.1k

really needed i to work with genome browser, cause this is for my colleagues, that only work with genome browser

ADD REPLYlink written 3 months ago by salamandra130
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1088 users visited in the last hour