[BioC] extract introns

Steve Lianoglou mailinglist.honeypot at gmail.com
Tue Nov 15 23:41:30 CET 2011

HI Yating,

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 ...


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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