excel linked with IGV to show regions

[kunbin qu]

Could somebody help me with this? I have an excel sheet with start and
end coordinates in each row (say, 1000 of them), when I browse through
row by row in the excel sheet, can it automatically be linked to the
IGV to show the region with my transcriptome data? I was told it could
be done with a macro in excel sheet. Does anybody have that done which
could be shared? Thanks.

-Kunbin
Genomic Health, Inc.
650-569-2070

[Cook, Malcolm]

Kunbin,

You have two options, one of which requires macro programming and one of which requires using Excel's hyperlink function.

Assuming Excel columns A,B,C contain labels chromosome,start,end in row 1.

Using hyperlink is easier.

1. Open IGV on your genome with whatever tracks you want loaded
2. following http://www.broadinstitute.org/igv/Preferences#Advanced - check "Enable Port 60151"
3. to your Excel sheet, add another column labelled IGV
4. Right below it, in row 2, enter the formula =hyperlink("http://localhost:6051//goto?locus="&A2&":"&B2&"-"&C2)
5. use Excel's "fill down" to copy that formula all the way to end of your data
6. click on your links

Pros/Cons:

* no macro programming needed
* no additional dependencies
* Requires clicking on the IGV column
* depending on browser & config, you may see your web browser flash by as it interprets the http link

If this meets your needs, then go with it

If you want

* not to add an additional column
* not to have to click on additional IGV column
* to control IGV when you move from line to line using, say arrow keys or the mouse, or when you hit a different key combination
* not to see your web browser flicker when you click on the IGV hyperlink

... then macro programming is needed, and installing additional library so Excel can communicate directly to IGV over port 60151. It works a treat, and is described in my blog at: http://malcook-gedanken.blogspot.com/2010/04/control-igv-from-excel-or-other.html

Let us know which you choose and how you fare....

Cheers,

Malcolm Cook
Stowers Institute - Kansas City

[Brent Pedersen]

(I'm not the OP, but)
Thanks Malcom, I didn't think of the trick of using localhost:port as a link!