are there any actively updated software suitable for FAIRE-seq (or DNAse-seq, which I believe poses similar problems) peak-calling?
I think I did 'homework' and it seems that MACS2 along with IDR is used quite frequently, but not all agrees it could handle broad peaks properly. I've used it and get quite reasonable peak numbers (usually tens, or hundreds thousands).
I've also used HOMER using
-style factor option, number of peaks are also reasonable (it depends of course on p/q-value used).
Installing/running ZINBA or F-seq failed at some point and it seems that both are abandoned.
What are your suggestions? Are you aware of any 'fresh' package for FAIRE/DNA-se seq? Allowing biological replication if possible.
Also, what is your view of summarizing biological replicates? Is IDR correct? How about comparing samples, are you seek unique peaks or take quantitative point of view and compare read number corresponding to shared peaks?
Best Regards, Maciej