how to visualize the bedgraph and bed file

Question

[Raghav]

I have generated bedgraph and bed files for the visualization. But I am unable to visualize it in WASHU browser.

It would be very helpful if anyone could help me to guide step by step to upload and visualize. I am using TAIR10 as a reference. I want to visualize my bed file and bedgraph file over the genome of A. thaliana.

thank you for your valuable comments in advance.

[Kizuna]

for bed file: UCSC genome browser is fine:

http://genome-euro.ucsc.edu/cgi-bin/hgCustom?hgHubConnect.destUrl=..%2Fcgi-bin%2FhgTracks&clade=mammal&org=Human&db=hg19&position=chr21%3A33%2C031%2C597-33%2C041%2C570&hgt.positionInput=enter+position%2C+gene+symbol+or+search+terms&hgt.suggestTrack=knownGene&hgsid=198096649_gqEJJU9RvA6ij92qw9GNUIohOAUB&pix=1260

More info: http://genome-euro.ucsc.edu/FAQ/FAQformat.html#format1

[Raghav]

Dear Kizuna,

At ucsc browser, I am unable to customize TAIR 10 (for Arabidopsis thaliana) may it is not located at UCSC browser.

but thank you for the effort

Answer 1

[Devon Ryan]

You could just download IGV and then import the tracks. That would be quite simple and you should have IGV around anyway if you ever deal with NGS datasets.

Answer 2

[Vitis]

Because we have a established genome browser based on GBrowse, this is pretty straightforward. I use wiggle2gff3.pl to convert bedGraph into wibs and a gff3 file pointing to those wibs. Then you'll use the GBrowse gff3 database for visualizing the tracks. It should be noted this way you reduced the resolution of the data, so it's only good for visualization but not quantitative analyses. The newer upgrade to this is to use BigWig perl module to handle these types of files.

Answer 3

[Alex Reynolds]

The WashU Epigenome Browser developer is pretty responsive to help requests — I've always been able to fix my issues with his guidance. You can reach him through the WashU community site.