visualization of ChIP-seq data sets in Gaggle

[marco mendoza]

Dear Gaggle users; developpers;

Im currently interested in using Gaggle for visualizing ChIP-seq
datasets, but I have realized that the list of supported formats does
not inlcude a tipical ChIP-seq format, namely a wiggle file format
(http://genome.ucsc.edu/goldenPath/help/wiggle.html).

Could some one let me know if you managed to circunvent such problem,
and how? and of course it would be quit kind of the developpers to
upgrade the available formats to that used in next generation
sequencing methods like wiggle or BED formats.

[cbare]

Hi Marco,

I have worked a bit w/ ChIp-seq datasets in the gaggle genome browser
- albeit only in the form of coverage. I agree that the track-import
options could use some attention. That's been on the list for a while
but not at the top, yet.

I usually use the R integration to import new tracks. R will let you
load just about any data type and format, transform it to the GGB's
preferred sequence/strand/start/end/value format, and add the new
track right into the GGB's database.

It's also possible to do the same transformation in the scripting
language of your choice or even Excel and output a tab-delimited file
w/ columns:

sequence - name of chromosome/plasmid/etc, must match names in GGB.
strand - one of +,-,.
start - an integer no greater than the length of the sequence
end - an integer no greater than the length of the sequence
value - a floating point measurement (intensity, log ratio, etc.)

You can reply with more specifics and I can probably help more. If
you'd like to send a small sample of your source data (or dummy data
that looks the same) I might be able to help transform it.

- Chris