Hi Valerie, 

Thanks for your response. I did try looking at the GEO location, but since the names of the 82 directories do not provide any information as to what files they contain (at least as far as I could tell), I did not proceed further with that:-P

I did try the pasillaBamSubset yesterday before I emailed the list, but I had problems reading the files using BamFileList. I tried:

---
> fls <- c("untreated1_chr4.bam", "untreated3_chr4.bam")
> path <- "/Library/Frameworks/R.framework/Versions/2.15/Resources/library/pasillaBamSubset/extdata/"
> bamlst <- BamFileList(fls, index=character())
> genehits <- summarizeOverlaps(chr4genes, bamlst, mode="Union")
Error in .io_check_exists(path(con)) : file(s) do not exist:
  'untreated1_chr4.bam'
---
I assume that it's because the path to the files (as stored in 'path') is not passed on to bamlst through BamFileList(?). The above was modified from the vignette, which reads:

----
> fls <- c("treated1.bam", "untreated1.bam", "untreated2.bam")
> path <- "pathToBAMFiles"
> bamlst <- BamFileList(fls, index=character())
> genehits <- summarizeOverlaps(chr4genes, bamlst, mode="Union")
----
I also tried supplying the full path to 'fls' like this:

fls <- c("/Library/Frameworks/R.framework/Versions/2.15/Resources/library/pasillaBamSubset/extdata/untreated1_chr4.bam", "/Library/Frameworks/R.framework/Versions/2.15/Resources/library/pasillaBamSubset/extdata/untreated3_chr4.bam")
bamlst <- BamFileList(fls, index=character())
genehits <- summarizeOverlaps(chr4genes, bamlst, mode="Union")

which works in the sense that the bams are read, but later yields a pretty messy 'design' matrix:
> design
 condition replicate        type                                                                                                   countfiles
1 untreated         1 single-read /Library/Frameworks/R.framework/Versions/2.15/Resources/library/pasillaBamSubset/extdata/untreated1_chr4.bam
2 untreated         3 single-read /Library/Frameworks/R.framework/Versions/2.15/Resources/library/pasillaBamSubset/extdata/untreated3_chr4.bam

And lots of warnings when applying 'summarizeOverlaps':

---
> genehits <- summarizeOverlaps(chr4genes, bamlst, mode="Union")
Warning messages:
1: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chr2L, chr2R, chr3L, chr3R, chr4, chrM, chrX, chrYHet
  - in 'y': chrchr3R, chrchrX, chrchr4, chrchr3L, chrchr2LHet, chrchrU, chrchrXHet, chrchr2RHet, chrchrdmel_mitochondrion_genome, chrchrYHet, chrchr2R, chrchr3LHet, chrchr3RHet, chrchr2L
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).
2: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chr2L, chr2R, chr3L, chr3R, chr4, chrM, chrX, chrYHet
  - in 'y': chrchr3R, chrchrX, chrchr4, chrchr3L, chrchr2LHet, chrchrU, chrchrXHet, chrchr2RHet, chrchrdmel_mitochondrion_genome, chrchrYHet, chrchr2R, chrchr3LHet, chrchr3RHet, chrchr2L
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).
---

>From what I understand the end results should be a 'CountDataSet' object for use in further downstream analysis, and it looks like I do end up with that:
---
> geneCDS
CountDataSet (storageMode: environment)
assayData: 82 features, 2 samples 
  element names: counts 
protocolData: none
phenoData
  sampleNames: /Library/Frameworks/R.framework/Versions/2.15/Resources/library/pasillaBamSubset/extdata/untreated1_chr4.bam
    /Library/Frameworks/R.framework/Versions/2.15/Resources/library/pasillaBamSubset/extdata/untreated3_chr4.bam
  varLabels: sizeFactor condition ... countfiles (5 total)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
  pubMedIds: 20921232 
Annotation:  
---
I'll look into how to query CountDataSets to see if it really worked. 

I would appreciate if someone could help me understand how to supply the path to bam files to BamFileList in a smarter way than I did above. I look forward to applying these great tools. 

And thank you everybody for your suggestions!

Best wishes, 
Darwin


On Jan 11, 2013, at 9:09 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
> 
> 
> 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@berkeley.edu
>> 
>> Please send Fedex packages to:
>> 163 Life Sciences Addition, attn: Harland lab room 571
>> 
>> 
>> 
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