[Bioc-sig-seq] NA vector for alignQuality with Bowtie output

[Martin Morgan]

Ramzi TEMANNI wrote:
> Hi,
> I'm loading bowtie aligned data using the following instruction:
> aln<- readAligned("./S1", pattern="S1_1.hg19.bowtie.align", type="Bowtie")
> but when i call alignQuality(aln), i get the following:
> class: NumericQuality
> quality: NA NA ... NA NA (4340867 total)
> Anyone have an idea why quality is NA ?

Hi  Ramzi --

Here's the description of Bowtie output

 http://bowtie-bio.sourceforge.net/manual.shtml#algn_out

there is no alignment quality reported.

Martin
> 
> Thanks in advance
> 
>> sessionInfo()
> R version 2.10.0 (2009-10-26)
> x86_64-pc-linux-gnu
> 
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
>  [1] doMC_1.2.0        multicore_0.1-3   foreach_1.3.0     codetools_0.2-2
>  [5] iterators_1.0.3   ShortRead_1.4.0   lattice_0.17-26   BSgenome_1.14.2
>  [9] Biostrings_2.14.8 IRanges_1.4.8
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.6.0 grid_2.10.0   hwriter_1.1   tcltk_2.10.0  tools_2.10.0
> 
> 
> Best Regards,
> Ramzi
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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PO Box 19024 Seattle, WA 98109

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Phone: (206) 667-2793