Dear Tatiana, You can use BED2RangedData to convert the BED format for annotatePeakInBatch. FYI, here is a list of FAQ about ChIPpeakAnno http://pgfe.umassmed.edu/ChIPpeakAnno/FAQ.html Best regards, Julie On 5/28/13 8:51 AM, "Subkhankulova, Tatiana" <t.subkhankulova@imperial.ac.uk> wrote: Dear Julie, I have read your ChIPpeakAnno user’s guide. It seems very helpful in annotation ChIP-seq peaks. However, I had a problem in generation of input data for the R-analysis. Would it be possible for you to let me know how did you make the object myPeakList? Did you use initially BED, TXT of any other format? Currently, I can get BAM, BED, WIG or TXT files, which contain information about ChIP peaks, though I do not know how transform any of them to R-input object. Please help, Many thanks in advance, Dr T Subkhankulova Heart Science National Heart and Lung Institute Imperial College Imperial Centre for Translational and Experimental Medicine, 3rd Floor Office 322, Lab 304 Hammersmith Hospital Campus Du Cane Road London W12 0NN Tel: +44(0)2075941825 E-mail: tsubkhan@imperial.ac.uk <mailto:tsubkhan@imperial.ac.uk> Mob: 07758370590 [[alternative HTML version deleted]]