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

[Darwin Sorento Dichmann]

Hi Dan, 

Thanks for your suggestion. I did look at the pasilla package before I emailed the list, but it doesn't seem to contain bam files:
----
lsa-579-005:~ darwin$ ls -l /Library/Frameworks/R.framework/Versions/2.15/Resources/library/pasilla/extdata
total 46184
-rw-r--r--  1 darwin  admin  13589253 Oct  2 13:04 Dmel.BDGP5.25.62.DEXSeq.chr.gff
-rw-r--r--  1 darwin  admin       552 Oct  2 13:04 geneIDsinsubset.txt
-rw-r--r--  1 darwin  admin    498373 Oct  2 13:04 pasilla_gene_counts.tsv
-rw-r--r--  1 darwin  admin   1370030 Oct  2 13:04 treated1fb.txt
-rw-r--r--  1 darwin  admin   1359480 Oct  2 13:04 treated2fb.txt
-rw-r--r--  1 darwin  admin   1361730 Oct  2 13:04 treated3fb.txt
-rw-r--r--  1 darwin  admin   1363665 Oct  2 13:04 untreated1fb.txt
-rw-r--r--  1 darwin  admin   1371149 Oct  2 13:04 untreated2fb.txt
-rw-r--r--  1 darwin  admin   1358790 Oct  2 13:04 untreated3fb.txt
-rw-r--r--  1 darwin  admin   1359414 Oct  2 13:04 untreated4fb.txt
-----

lsa-579-005:~ darwin$ head /Library/Frameworks/R.framework/Versions/2.15/Resources/library/pasilla/extdata/treated1fb.txt 
FBgn0000003:001	0
FBgn0000008:001	0
FBgn0000008:002	0
FBgn0000008:003	0
FBgn0000008:004	1
FBgn0000008:005	4
FBgn0000008:006	1
FBgn0000008:007	18
FBgn0000008:008	4
FBgn0000008:009	16

Or are those '*fb.txt' files some sort of "debinaried" bam files?

Again, thanks for your suggestion. 

Best wishes, 
Darwin 


On Jan 10, 2013, at 9:38 PM, Dan Tenenbaum wrote:

> 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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