Regarding the ChIPpeakAnno Package
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 4 months ago
United States
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]]
Annotation Annotation • 692 views
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Ayush Raman ▴ 20
@ayush-raman-4609
Last seen 9.6 years ago
Hello Prof. Julie, I was able to run the script. I found bug in my program. I was having problems converting my bed into the ranged data. Thanks for replying me back. Regards, Ayush Raman Bioinformatics Research Scientist Institute for Systems Biology Seattle WA 206-732-1473 On Thu, Apr 21, 2011 at 8:47 AM, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu>wrote: > 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]]
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