Entering edit mode
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
[[alternative HTML version deleted]]