Does anyone here has had any experience using GC content isochores in GAT? It would be great to hear your experiences with this feature.
Issues with isochores
Using isochores is not very well documented in the manual and I'm having trouble determining how to build and use the input file. I found that GAT enrichments values change depending on the window size in my input isochore files (e.g. 500bp versus 5Kb windows). I'm mot sure if this is because I'm not inputting data correctly or if it's related to multiple testing or statistical power issues because of the number of regions.
Isochores affect genomic enrichments
To test how using the isochores file affect enrichments, I ran GAT with shuffled isochores (permuting the 4th column below). This decreased the magnitude of my enrichments, which is what I would expect from the decrease in power from adding one extra variable into the analyses.
Making an isochores file
The only way I found it possible to make GAT even accept the input isochore file without crashing is outlined below. Fourth column is an integer value from 1-N, where N in this case is 8 and correspond to the GC content 8-tile which the BED file entry belongs too (they used N=8 in the original paper).
chr1 50000 100000 1 chr1 100000 150000 2 chr1 350000 400000 1 chr1 400000 450000 2 chr1 550000 600000 2 chr1 600000 650000 1 chr1 650000 700000 2 ...
For more details on what works and doesn't work, see my post here.
Any thoughts would be greatly appreciated!