[Bioc-sig-seq] .gff from AlignedRead

[Martin Morgan]

On 03/19/2010 03:46 PM, joseph wrote:
> Hi
> is there a way to export a gff file from an AlignedRead object as it is done from coverage?

rtracklayer::export takes a RangedData object. You can create a
RangedData object from an AlignedRead object is a line or so of code,
along the lines of

  library(ShortRead)
  example(readAligned)
  rd = RangedData(IRanges(position(aln3), width=width(aln3)),
                  space=chromosome(aln3))

(and maybe other columns) and then

  library(rtracklayer)
  export(rd, "my.gff3")

Martin

> Thanks
> Joseph
> 
> 
> 
>       
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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