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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