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 ?

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

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