There seem to be precious few published FAIRE-seq studies to date that would suggest best practice, so I have the following questions:
Is anyone out there actively or recently performed FAIRE-seq analysis?
Which tools are giving the best results?
This may be a lack of understanding on my part, but although it seems as though input controls are un-necessary, I still remain to be convinced controls are not required - any thoughts?
Thanks in advance!
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Ian
You are right, there are few publications out there. I was briefly involved with analyzing FAIRE-seq data in the ENCODE project. It couldn't hurt to check out ENCODE's best practice guidelines.
In the project I was involved in, FSeq (a general density estimator) was initially used and was OK, but the group of one project leaders then developed ZINBA which they felt worked slightly better for FAIRE-seq and DNase-seq.
The encode project refers to http://www.uwencode.org/proj/hotspot-ptih/ for most of the tracks (especially dnaseI sites) however most of the code is not available; i got it working up to hotspot calling but FDR calculations and peak calling are not publicly available.
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