This overlap is strand specific, I think. You'll need to have '*' as strand in one of them.
Michael On Fri, Dec 10, 2010 at 11:56 AM, Jason Lu <[email protected]> wrote: > Hi, > > First thank developers for building so many cool tools for HTS. > I have a question which I would like to have someone give me an hint > or two. Thanks. > > Here I have , > > countOverlaps(cds[1],aln) > 2 > > I kind of expect the answer should be 6. Any idea? > > > aln > GappedAlignments of length 6 > rname strand cigar qwidth start end width ngap > [1] chr19 + 33M 33 58858743 58858775 33 0 > [2] chr19 - 33M 33 58858812 58858844 33 0 > [3] chr19 + 33M 33 58858912 58858944 33 0 > [4] chr19 - 33M 33 58858921 58858953 33 0 > [5] chr19 + 33M 33 58858934 58858966 33 0 > [6] chr19 + 33M 33 58858940 58858972 33 0 > > > cds[1] > GRangesList of length 1 > $1 > GRanges with 8 ranges and 2 elementMetadata values > seqnames ranges strand | cds_id cds_name > <Rle> <IRanges> <Rle> | <integer> <character> > [1] chr19 [58858388, 58858395] - | 185127 NA > [2] chr19 [58858719, 58859006] - | 185128 NA > [3] chr19 [58861736, 58862017] - | 185129 NA > [4] chr19 [58862757, 58863053] - | 185130 NA > [5] chr19 [58863649, 58863921] - | 185131 NA > [6] chr19 [58864294, 58864563] - | 185132 NA > [7] chr19 [58864658, 58864693] - | 185133 NA > [8] chr19 [58864770, 58864803] - | 185134 NA > > > seqlengths > chr1 chr2 ... chr18_gl000207_random > 249250621 243199373 ... 4262 > > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > > 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 datasets utils methods base > > other attached packages: > [1] GenomicFeatures_1.2.0 Rsamtools_1.2.1 Biostrings_2.17.48 > [4] GenomicRanges_1.1.38 IRanges_1.7.40 > > loaded via a namespace (and not attached): > [1] Biobase_2.9.2 biomaRt_2.6.0 BSgenome_1.17.7 DBI_0.2-5 > [5] RCurl_1.4-4 RSQLite_0.9-2 rtracklayer_1.10.1 tools_2.12.0 > [9] XML_3.2-0 > > Many thanks! > > Jason > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
