can I use homer findpeaks -style dnase to analyse Faire-seq file?

Question

[Ming Lu]

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 1

[Kevin Blighe]

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