[BioC] extract introns
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Tue Nov 15 23:41:30 CET 2011
On Tue, Nov 15, 2011 at 4:48 PM, Yating Cheng <yating.cheng at charite.de> wrote:
> Hi, steve
> Thanks for your answer. About converting the names of chromosome, it is
> kind of difficult.
> I need the intron sequences for every gene, but the chromosome names of
> some genes I got from biomart are the same.
Sorry, I'm confused.
What organism are you working with?
Can you construct a TranscriptDb for it using the GenomicFeatures
package (you'll have to read through the GenomicFeatures vignette).
> I am not sure about how can I get specific genes from BS genome, and match
> them to gene-IDs.
BSgenome packages do not have gene specific information, they only
contain sequence information for different organisms.
The fact that you can use a BSgenome.* package for your organism of
interest suggests that you should be able to build a TranscriptDb for
it, so that's good news ...
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| Weill Medical College of Cornell University
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