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

[Valerie Obenchain]

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


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
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> Molecular and Cell Biology
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