[BioC] extract introns

[Martin Morgan]

On 11/09/2011 03:22 AM, Yating Cheng wrote:
> Dear Bioconductor Memebers,
>
> Now I have to extract intron sequences, I have already exon+intron, intron
> sequences. Someone told me that I can use Biostring. But I tried, it
> failed.
>
> Do you know how to use Biostring to solve this problem, or is there any
> other possibility to solve this problem?

Steve and Ivan mention GRanges + BSgenome. I wanted to mention 
Rsamtools::FaFile with indexFa, which allows input of DNA sequence from 
fasta files rather than BSgenome packages. You gain flexibility in terms 
of where the sequence comes from, but lose BSgenome features like 
masking and data management.

Martin

>
> Thanks very much.
>
> Best Regards
>
> Yating Cheng
>
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