[BioC] Pasilla data for "Counting with summarizeOverlaps/GenomicRanges"

[Dan Tenenbaum]

On Thu, Jan 10, 2013 at 9:26 PM, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
> 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.
>

You might also look at the pasilla package.
Dan


> On Fri, Jan 11, 2013 at 12:13 AM, Paul Shannon <pshannon at 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 at berkeley.edu
>> >
>> > Please send Fedex packages to:
>> > 163 Life Sciences Addition, attn: Harland lab room 571
>> >
>> >
>> >
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>> >
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