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 <jasonlu68@gmail.com> 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
>
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>

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