[BioC] shortread readAligned with BWA

[Nathalie Conte]

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









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