Uploading narrowPeak Annotation Files to display on UCSC Genome Browser

Question

[Kevin.Y]

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?

[microfuge]

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,.

[Kevin.Y]

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

[microfuge]

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.

[GenoMax]

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

[Sinji]

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.

[GenoMax]

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

[Kevin.Y]

Yes it follows the format.

Answer 1

[a.abnousi]

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!