Hi, I'm currently comparing the alignment generated by bowtie and maq on the data used in the HilbertVis pdf file of the ShortRead package (NCBI SRA accession: SRA000206). From the original .seq and .prb solexa files, I have generated the fastq files and aligned them to the ref. genome using bowtie and maq.
I load both map files in R using readAligned. Then when filtering my reads, I realized that most of the default filter functions have been written for maq and are therefore not necessarily available for bowtie. I'm actually interested in the alignQualityFilter in order to sort those reads which map several times in the genome (as described in the page 22 of the "I/0 and Quality Assessment using ShortRead" of last November bioC tutorial session). But, this method relies on the quality slot of the object returned by the alignQuality accessor, which is NA in the case of a bowtie alignment. This is actually normal, as the final quality mapping value stored in this object is only available in the maq map file and now in the bowtie one. So I'd just would like to know if there would be another way to filter out the reads mapping multiple times in the genome when using an AlignedRead object obtained from a bowtie map file. Sorry that this sounds quite confusing... Here is the actual code and what happens: filt <- alignQualityFilter(threshold=1) # works aln<-readAligned( "H3K4me1", "run13_lane4.map", type="MAQMap", filter=filt) # fails aln2<-readAligned( "H3K4me1.bowtie", "run13_lane4.map", type="Bowtie", filter=filt) Error in x...@ranges[i] : subscript contains NAs Any ideas how to filter a bowtie type alignment for reads mapping multiple time in the genome? Cheers, N. > sessionInfo() R version 2.9.0 Under development (unstable) (2009-01-04 r47472) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] HilbertVis_1.1.4 ShortRead_1.1.33 lattice_0.17-20 BSgenome_1.11.8 [5] Biobase_2.3.9 Biostrings_2.11.22 IRanges_1.1.33 loaded via a namespace (and not attached): [1] grid_2.9.0 Matrix_0.999375-17 tools_2.9.0 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
