[BioC] Is there a package that maps short sequence to exon?

[Martin Morgan]

On 06/15/2012 11:08 AM, ying chen wrote:
>
>
>
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> Hi guys, I just wonder if there is any Bioconductor package that can
> take a short nucleotide sequence (25 mer) or its genomic coordinate
> (chr&  pos) as input and return exon number it maps to? Thanks a lot

Take a look at GenomicRanges / GenomicFeatures, you might read your 
alignments as readGappedAlignments, or just create a GRanges() object,

   library(GenomicRanges)
   reads = GRanges(c("chr1", "chr7"),
       IRanges(start=c(12614, 195554), width=1))

and then use a package like TxDb.Hspaiens

   library(TxDb.Hsapiens.UCSC.hg19.knownGene)
   ex = exons(TxDb.Hsapiens.UCSC.hg19.knownGene)

and findOverlaps

   hits = findOverlaps(reads, ex)

to discover that your 'query' (reads) overlaps the exons

 > queryHits(hits)
[1] 1 1 2
 > values(ex)$exon_id[subjectHits(hits)]
[1]     5     2 98786

Martin

> for the help! Ying Chen [[alternative HTML version deleted]]
>
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