Ayush,

Please send the code snippet and session information. I think you used output=”both” and multiple=TRUE that resulted in outputting all overlapping features to the 30 peaks. Please type ?annotatePeakInBatch to see the meaning of the parameters. Thanks!

Best regards,

Julie


On 4/18/11 8:27 PM, "Ayush Raman" <Ayush.Raman@systemsbiology.org> wrote:

Hello Prof. Zhu,

I am interested in the chip-seq annotation that has been defined in your BMC Bioinformatics journal paper. I was using the package to annotate the peaks for one of my chip-seq experiments. My input file is a bed file from the MACS output. I followed the steps for the saving the annotated peaks as an Excel file. When I opened the file, I was having some confusions which are as follows:

1.  Suppose if "space" means chromosome, "start" means the start of the peak, "end" means the end of the peak in the output Excel file. I didn't understand why I don't get the same start and end co-ordinates of the peaks in my output file as compared to my input files.

2. Also, can you explain why I am getting more than 12000 annotations for only 30 peaks.

I am sending the input and output files as as attached document.

Thanks.
Ayush Raman
Bioinformatics Research Scientist
Institute for Systems Biology
Seattle WA
206-732-1473



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