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]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
