Question: GAT - using GC isochores: correct formatting and statistical implications
gravatar for Ricardo A.
2.3 years ago by
Ricardo A.90
University of Michigan Ann Arbor, MI - USA
Ricardo A.90 wrote:


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!


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