What Is The Best Software For Finding Footprints In Mouse Dnase-Seq Data?

Question

[spacemorrissey]

What is the best software for finding footprints in mouse DNase-seq data? Many of the papers on identifying small regions protected from DNase I cleavage by a bound transcription factor do not seem to make their software available. I have looked at CENTIPEDE, but the approach of starting with motif instances seems backwards to me. I would rather find the footprints and look for motifs within them. Thanks.

Answer 1

[jpiper]

I've just published a paper in NAR describing a new footprint searching algorithm, and more importantly a software implementation of the method, which is really easy and fast to use (here's the documentation describing the builtin scripts). Feel free to email me (my contact details are on the documentation) if you need any help.

Answer 2

[aboyle]

There seem to be 3 main methods right now. Unfortunately, CENTIPEDE is the only one with an actual software package released. The benefit of their training on specific motifs is that there appears to be a unique DNase cutting pattern for each TF. This potentially allows for a more accurate prediction of the TF binding. In reality, I don't think the sequencing depth is such that you actually see the average pattern at each site. There is also the HMM method from Duke (in the same GR issue as CENTIPEDE) but that has no released software because the training was essentially impossible to automate. I happen to think that this is a great method though... Finally, there is the method from the Stamatoyannopoulos which is a little simpler to implement and is also invariant to the PWM.

I do think there are some 2nd gen methods in the pipeline though... we'll see.

Answer 3

[dnaseiseq]

You might be interested in trying the DNaseR package, which will be released in the upcoming version of Bioconductor.

DNase I footprinting analysis of DNase-seq data

http://bioconductor.org/packages/devel/bioc/html/DNaseR.html

Answer 4

[biorepine]

Did you try F-Seq ?

[spacemorrissey]

Yes, I use Fseq to find peaks or nucleosome depleted regions, but I it will not let me look within those high signal regions to identfy short segments(6-40bp) protected from DNase cleavage by a stably bound TF.