Thank you Julie,

I misunderstood the functionality and thought I was a "de novo" motif
finder...
Any insight on how to predict motifs from ChIPseq experiments? Any R module
that does it and you can recommend? May you think of implementing this
function to your awesome package?
;)

JL

2013/2/27 Zhu, Lihua (Julie) <Julie.Zhu@umassmed.edu>

> Jose,
>
> Thanks for the inquiry! I will add the following to the documentation.
>
> The examplePattern.fa, in fasta format, is included in the package as an
> example pattern file for running function summarizePatternInPeaks. To use
> this function, you will need to create your own custom pattern file with
> the
> pattern(s) you are interested in searching in the peaks.
>
> The pattern file is in fasta file format. The base in the pattern consists
> of IUPAC designated nucleotide symbols such as A, C, G, T, N, V, H, D....
>
> The bottom table on http://pgfe.umassmed.edu/ZFPsearch.html lists the
> abbreviation codes for degenerate bases.
>
> Best regards,
>
> Julie
>
>
> On 2/27/13 10:54 AM, "José Luis Lavín" <joluito@gmail.com> wrote:
>
> > When looking for motif occurrence in the peaks, the "examplePattern.fa"
> file
> > you supply with the module:
> >
> > -Is a standard example pattern file you can use for any set under
> analysis or
> > is it a custom one you include in the package referred to a particular
> set of
> > motifs?
> >
> > -May you give a hint on how to create such kind of file myself?
> >
> > Thanks in advance
> >
> > JL
> >
> >
> >
> >
>
>


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