The original poster seems to be referring to a line in the pasilla vignette

The SAM alignment files from which \Rpackage{pasilla} was generated are
available at \url{http://www.embl.de/~reyes/Graveley/bam}.

and indeed it seems this link is dead.  but it doesn't really matter for
the vignette as the
pasillaBamSubset package has the bam files needed.

On Fri, Jan 11, 2013 at 12:13 AM, Paul Shannon <pshannon@fhcrc.org> wrote:

> Hi Darwin,
>
> Please give us a little bit more detail on the tutorial you wish to
> follow.   Is it one of the vignettes that accompany GenomicRanges?
>
> Also, your sessionInfo() may provide indispensable clues allowing us to
> help out.
>
> Thanks -
>
>  - Paul
>
> On Jan 10, 2013, at 8:33 PM, Darwin Sorento Dichmann wrote:
>
> > Greetings,
> >
> > I wish to follow the tutorial for summarizeOverlaps from GenomicRanges,
> but the pasilla.bam files ("treated1.bam", "untreated1.bam",
> "untreated2.bam") are not with in the package and the provided link for
> download is dead (http://www.embl.de/~reyes/Graveley/bam).
> >
> > Anybody know where I can get those data or have a copy? I also tried
> following the GEO accessions from the original publication, but all I found
> was GFFs and BEDs, no bams.
> >
> > Any help is greatly appreciated.
> >
> > Best,
> > Darwin
> > ________________________________
> > Darwin Sorento Dichmann, M.S., PhD
> > University of California, Berkeley
> > Harland Lab
> > Molecular and Cell Biology
> > 571 Life Sciences Addition
> > Berkeley, CA 94720
> > Phone# (510) 643-7830
> > Fax# (510) 643-6791
> > E-mail: dichmann@berkeley.edu
> >
> > Please send Fedex packages to:
> > 163 Life Sciences Addition, attn: Harland lab room 571
> >
> >
> >
> >       [[alternative HTML version deleted]]
> >
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