[BioC] shortread readAligned with BWA

[Martin Morgan]

Hi Nathalie 

I think your bam files are too large for your version of R! I suggest using the development version of R then biocLite('ShortRead') then trying again. Martin
-- 
Martin Morgan

On Aug 19, 2011, at 16:47, Nathalie Conte <nac at sanger.ac.uk> wrote:

> HI,
> 
> I am trying to use ShortRead to get QCs on my bam files ( aligned with BWA)
> this is what I used to read my aligned files
> > read_bam<-readAligned(".",pattern="bam",type="BAM")
> then I have this error:
> Error: Input/Output
> 'readAligned' failed to parse files
> dirPath: '.'
> pattern: 'bam'
> type: 'BAM'
> error: negative length vectors are not allowedshortread
> I saw on a previous bioconductor  mailing list that Martin Morgan gave some previous clues about this kind of error  and advised to  check the Bam using these commands
> #### Martin Morgan <http://search.gmane.org/?author=Martin+Morgan&sort=date> | 8 Oct 18:59
> Favicon
> 
> 
>   Re: Illumina QC using ShortRead
> 
> Can you (a) try to read the
> bam file directly using
> 
> param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE,
>   what = ShortRead:::.readAligned_bamWhat())
> 
> res = scanBam('./100927_s_1.bam', param=param)
> 
> I think this will fail, and then
> 
> traceback()
> 
> 
> 
> #### 
> If I do this, I get this kind output :
> 
>> param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE,
>  what = ShortRead:::.readAligned_bamWhat())
>> res = scanBam('./6160_7#16.bam', param=param)
> Error in .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) :
> negative length vectors are not allowed
>>  traceback()
> 4: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...)
> 3: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = param)
> 2: scanBam("./6160_7#16.bam", param = param)
> 1: scanBam("./6160_7#16.bam", param = param)
> 
> 
> Could somebody advise on the best way to go forward?My Bams don't seem to be right for ShortRead, Do I need to realign my reads?
> Many thanks
> Nathalie
> 
> 
> 
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
> 
> locale:
> [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=C              LC_MESSAGES=C
> [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] ShortRead_1.6.2     Rsamtools_1.0.8     lattice_0.18-8
> [4] Biostrings_2.16.6   GenomicRanges_1.0.4 IRanges_1.6.13
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0 grid_2.11.1   hwriter_1.3   tools_2.11.1
> 
> 
> 
> 
> 
> 
> 
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
> 
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