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

[Martin Morgan]

On 01/11/2013 09:09 AM, Valerie Obenchain wrote:
> Hi Darwin,
>
> As Vince mentioned, the bam files are no longer available at the location
> specified in the summarizeOverlaps vignette. This location was taken from the
> DEXSeq vignette which has since been updtated to point to the GEO location,
>
> http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE18508
>
> Available file types include GFF, SAM and BEDGRAPH. The SAM can be easily
> converted to BAM with samtools
>
> samtools view -h -o outputFile.sam inputFile.bam

and Rsamtools::asBam

Martin

>
>
> As an fyi, we have a Bioconductor data package 'pasillaBamSubset' which includes
> a portion of chromosome 4 from the untreated1 (single-end) and untreated3
> (paired-end) files. You may find these smaller files useful for testing.
>
> Thanks for the reminder of the dead link. I will update the vignette.
>
>
> Valerie
>
>
>
> On 01/10/2013 08:33 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
>>
>>
>>
>>     [[alternative HTML version deleted]]
>>
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