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