[BioC] ChIPpeakAnno - for genes with multiple isoforms

[Zhu, Lihua (Julie)]

Hatice,

That is a great question! I would suggest you use transcript annotation file
instead of gene annotation file to annotate your peak. The transcript
annotation file should include multiple transcription start sites for genes
with multiple isoforms.

To obtain the transcript annotation using ChIPpeakAnno, you would use
function getAnnotation(mart, featureType="transcript"). Alternatively, you
could directly call annotatePeakInBatch using your own annotation file.

Thanks for the positive feedback!

Best regards,

Julie 


On 10/12/11 9:14 AM, "Hatice Ulku Osmanbeyoglu" <uosmanbey at gmail.com> wrote:

> Hello,
> 
> Thank you for this great tool.
> 
> I am using ChIPpeakAnno to annotate the ChIP-seq datasets. Our
> collaborators raised a question how  ChIPpeakAnno  handle annotation
> when genes have multiple isoforms including some with different
> transcription start sites.
> 
> If you give me some information regarding to this, it would be great.
> 
> Best,
> Hatice