Question: Uploading narrowPeak Annotation Files to display on UCSC Genome Browser
0
gravatar for Kevin.Y
3.1 years ago by
Kevin.Y10
Kevin.Y10 wrote:

I am trying to upload my narrowPeak annotation files onto the genome browser. I have uploaded the files by FTP, but every time I try to add my custom tracks onto the genome browser by pasting the url, I get the following error message: Error Unrecognized format type=narrowPeak line 2 of custom track.

Has anyone been able to upload narrowPeak annotation files successfully?

ADD COMMENTlink modified 9 months ago by a.abnousi30 • written 3.1 years ago by Kevin.Y10
1

I use a custom version of the ucsc browser and had this problem with a bam file. It was not compiled with support for that track type. Are you using the original UCSC browser or a clone/custom_installation,.

ADD REPLYlink written 3.1 years ago by microfuge1.3k

I'm using a custom version of the browser that is associated with the department. How did you overcome your problem?

ADD REPLYlink written 3.1 years ago by Kevin.Y10

The browser code needs to be redownloaded/recompiled with the support for that track. That seems to be the only solution other than using the original ucsc website.

ADD REPLYlink written 3.1 years ago by microfuge1.3k

Neat solution. Would be hard to figure out without this kind of first-hand information.

ADD REPLYlink written 3.1 years ago by genomax71k

I know this doesn't answer your question, but i've never really liked how difficult it is to upload files to the UCSC browser. So maybe you should take a look at IGV.

ADD REPLYlink written 3.1 years ago by Sinji2.9k

Test example provided by UCSC still works so the format is supported. Does your file follow the format?

ADD REPLYlink written 3.1 years ago by genomax71k

Yes it follows the format.

ADD REPLYlink written 3.1 years ago by Kevin.Y10
0
gravatar for a.abnousi
9 months ago by
a.abnousi30
a.abnousi30 wrote:

I had the same problem. What I did was copied the track information on one line rather than two.

track name='ChIP-Seq_peaks' description='ChIP-Seq peaks' type=narrowPeak visibility=3 db=hg38

and it worked. Strange!

ADD COMMENTlink written 9 months ago by a.abnousi30
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