Adding separate normalisation factor for size difference between input and treatment about macs

[taoliu]

Thanks for the suggestion! Will try to add these options later.

Tao

On Nov 21, 2013, at 3:57 PM, dav7mx [email protected] wrote:

Just to revive an issue that has been commented before. It has been shown that for some datasets (particularly those with larger depths) the normalization between the Input and the IP has a criticall effect in the FDR calculation. There have been some attempts to develop estimations for the normalizing factor that seem to work nicely with a wide range of sequencing depths (see for example: http://www.biomedcentral.com/1471-2105/13/199).

I've seen some forks from version 1.4 that include an option to give your own normalization factor (instead of using the linear normalization with --to-large or --down-scale). I think it would be great if such an option could be included in the main macs2 callpeak code (and not terribly complicated as far as I can tell). What do you think?

Best, and thaks for the program!

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[taoliu]

Included in 70fa25a