Does FACETS support non-human organisms?

[hongenxu]

Hi,
can FACETS support non-human organisms? I want to apply FACETS to my own chicken data, is it possible?

Best,
Hongen

[veseshan]

The current version supports mouse in addition to human. There is a GC normalization step in the log-ratio computation which uses the GC percentanges of the organism (and specific genome build). So while you can't use the package as is for chicken data, it could be modified to work.

Venkat

[hongenxu]

Hi Venkat,

thanks for your quick reply. I noticed that FACETS depend on https://github.com/mskcc/pctGCdata, and I can create this data set for chicken. I will try to figure out how to modify the scripts.

Best regards,
Hongen

[veseshan]

I will try to add a user_specified genome build as an option.