Hi Martin, Thanks for the info, I was mixing between reads quality and alignment quality Indeed there' no info about alignment Quality on bowtie output and reads quality could be extracted using quality() accessors.
I'm trying to generate mate pair data from single read data by aligning single reads (1/2) then look at the id and recover aligned pairs based on their ID. I'm trying to find out structural variations mainly fusion genes where mate 1 & 2 belong to different chromosomes. I'm trying to filter the data by keeping only pairs belonguing to diffrent chromosomes, but the final number is high around 20000 reads and it's very high so i'm looking for further filtering to remove artefact from there. Regards, Ramzi ---------------------------------------------------------------- On Tue, Dec 1, 2009 at 1:33 PM, Martin Morgan <[email protected]> wrote: > 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 > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
