On Sun, May 10, 2009 at 7:13 AM, Wu, Xiwei <XWu@coh.org> wrote:

> Hi,
>
> I have aligned some Solexa RNA-seq data to refseq mRNA sequences. The
> aligned location in the alignment report is relative to each refseq sequence
> start. Is it possible to map the aligned results back to genome with current
> available tools in Bioocnductor? In other words, I want to convert the
> alignment position relative to genome location. It is relatively easy for
> the exon sequences, but it is more complicated for the ones aligned to the
> splicing junction. I think this is doable in R, but I just want to check to
> see if there is already such a function avavilable. Thanks in advance.
>

There isn't any high-level functionality like this in Bioconductor, as far
as I know. It could probably be done fairly efficiently using the overlap
functionality in IRanges. One trick would be to create a new coordinate
system so that you can map all of the reads to exons in a single call to
overlap(). In other words, virtually concatenate all of the transcripts,
adding the appropriate offset to each read. Calling ranges() on the
overlap() result gives you the intersecting part of the overlap. Then
transform those coordinates to the genome. Essentially, you'll end up with a
set of genomic ranges and an integer vector with the original read index for
each range. Obviously, there were be duplicate indices whenever a read hit a
splice junction.


> Xiwei
>
>
>
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