Viewing Chip-Chip Data Within A Genome Browser

Question

[timjoncooper]

Hi!

We've currently got some processed ChIP-chip data within an .xlsx file - is there anyway this data can be converted for viewing on a genome browser? It currently contains the specific chromosomal loci the signal was probed and the signal strength for each protein investigated.

Thanks

• TC

[Arnaud Ceol]

Could you provide some example of data you want to convert (e.g. a few lines of your xlsx file)?

Answer 1

[Emily]

Hi Tim

There's some help here on adding custom tracks to Ensembl: documentation and video. The documentation lists the different kinds of file types that you can use and you can click on them to get the specs. I think a Bedgraph might be suitable for the kind of data you have, although without seeing your data I can't be certain.

Emily

[timjoncooper]

I've attempted to create a BedGraph file however when uploading it to the UCSC Genome Browser it returns the error: Unrecognized format type=bedGraph - what is causing this?

[Emily]

I have no idea about using UCSC, I can only help you with Ensembl. What species is your data in?

I just did a test using *S. cerevisiae* in Ensembl Genomes and it worked well. I made a guess on species because your chromosome was numbered I, rather than 1 and I knew S. cerevisiae had roman numeral numbered chromosomes. Even if I was wrong, it proves that it works.

[bede.portz]

If you are attempting to load data that was mapped to a different build of the genome than the one you are attempting to use in your browser session, you could get an error message. For example, your reads were mapped to the mm9 version of the mouse genome, but the UCSC browser defaults to the more recent mm9. Additionally, if you have reads that map outside the annotated ends of chromosomes, you can get an error message. HOMER has a tool to remove these so called "out of bounds" reads. Check out this link. http://biowhat.ucsd.edu/homer/ngs/ucsc.html

[Emily]

I think the issue is that he's followed the Ensembl documentation to produce the file, then tried to upload to UCSC. Different browsers will have slightly different requirements, so UCSC doesn't accept the Ensembl-compatible file. As I've shown, it works perfectly in Ensembl.

[timjoncooper]

This is the BedGraph file that I am using - it returns numerous errors.

https://www.dropbox.com/s/vzir2qpi2xolosu/chr1rec114.bedgraph

[Neilfws]

"The file you're looking for has been deleted or moved" ?

Answer 2

[Ian]

If all you want to do is view where the binding regions are in UCSC then just reformat columns to make a sheet that contains:

track name="chip-seq" description="longer description" 
chr   start   end  
chr   start   end 
etc..

Then save as tab delimited plain text. You can upload the file via the "manage custom tracks" button underneath the main view. You can display more information by extending the BED format. I like using narrowPeak format as you can simultaneously display the binding region and summit.