Question: can I use homer findpeaks -style dnase to analyse Faire-seq file? or which style is better or no style suite for Faire analysis?
just in this way:

findpeaks ${id%%.*}/ -i ctrl/ -style dnase > ${id%%.*}.Fairepeak.txt

attached all the style in homer findpeaks

findPeaks has 7 basic modes of operation:

factor

Peak finding for single contact or focal ChIP-Seq experiments or DNase-Seq. This type of analysis is useful for transcription factors, and aims to identify the precise location of DNA-protein contact. This type of peak finding uses a FIXED width peak size, which is automatically estimated from the Tag Autocorrelation. (see below)

histone

Peak finding for broad regions of enrichment found in ChIP-Seq experiments for various histone marks. This analysis finds variable-width peaks. (see below)

super

Find Super Enhancers in your data (see below)

groseq

De novo transcript identification from strand specific GRO-Seq. This attempts to identify transcripts from nascent RNA sequencing reads. (see below)

tss

Identification of promoter/TSS from 5'RNA-Seq/CAGE or 5'GRO-Seq data. More info in the TSS section.

dnase

Adjusted parameters for DNase-Seq peak finding. (NOTE: this is only for tag-style DNase-Seq) More info in the DNase section.

mC

DNA methylation analysis - documentation coming soon...

Answer: As nobody has responded, I wanted to add my own piece.

I'm familiar with both techniques and know that they are similar in the sense that they both principally aim to target DNase I hypersensitive sites (although FAIRE can be used for other markers). That said, I don't know the exact differences in pull-down methods in both techniques, and whether, for example, read coverage or region size (covered by reads) would differ between both. In that sense, I would advise ***not*** to use `-style dnase` for your FAIRE data.

Sure enough, I have just done some searching and it is even recommended on the HOMER website to not use `-style dnase` for FAIRE.

> **Two Different Types of DNase-Seq (Important!)**

> So far, there have been
> two heavily used protocols for DNase-Seq. The original method from
> the Crawford lab first ligates an adapter to the end of DNase-cleaved
> DNA fragments, and then sequencing into the fragment, often creating a
> "tag" in the process. The 2nd method involves extracting
> DNase-treated DNA and then size selecting for fragments of size
> ~50-100 bp. In the 2nd case, the idea is that open chromatin regions
> are likely to generate DNase cleavage sites less than 100 bp apart
> (creating a sub-100 bp fragment of DNA, say on either side of a
> transcription factor binding site), while nucleosomal DNA will likely
> produce fragments >150 bp (the size of a nucleosome). The first
> method is more faithful to the recovery of DNase cleavage sites, but
> the 2nd method shows very robust enrichment at regulatory elements and
> looks "cleaner". That comes with the catch that the 'open' regulatory
> element must be of a certain size range and capable of generating
> cleavage sites in the right size range. I'll refer to these as the
> "crawford method" and "size-selection method" to keep them straight.
>
> Why is this important? The original Crawford method measures DNase
> cleavage sites (and the strand information is less important), while
> the size-selection method is a lot like ChIP-Seq where the regulatory
> element with transcription factor binding sites is likely to be on the
> fragment of DNA extracted in the size selection process. In fact,
> DNase-Seq generated with the size-selection method should be treated
> exactly the same way in HOMER as ChIP-Seq data.

*[source: http://homer.ucsd.edu/homer/ngs/dnase/index.html]*

If you want me to summarise this for you: the HOMER author refers to the 'Crawford method' (original DNase-seq) and the 'size-selection method' (FAIRE-seq). The author relates exactly what I stated in my response (above), i.e., the pull-down method is different and thus region size covered by reads.

The source page to which I linked goes through the tutorial for analysing both.

Good luck,

Kevin