Thanks for developing and providing continued support for these tools! I am using v3.7.2 to analyze some HiChIP data, and I have a question about the hicAggregateContacts function. I can run this function using the parameters defined below and I get the tif image and the contact pair output.
Hello hicExplorer team!
Thanks for developing and providing continued support for these tools! I am using v3.7.2 to analyze some HiChIP data, and I have a question about the
hicAggregateContactsfunction. I can run this function using the parameters defined below and I get the tif image and the contact pair output.hicAggregateContacts -m matrix.mcool -o matrix.tif --BED bedfile.bed --mode intra-chr --transform total-counts --operationType sum --numberOfBins 21 --outFileContactPairs outputContactsMy question is: Is there a way to grab the values for the bins/pixels in the .tif plot, in a way to calculate the Aiden lab/ENCODE "APA" score? see Section II.a2 in this pdf: https://www.encodeproject.org/documents/75926e4b-77aa-4959-8ca7-87efcba39d79/@@download/attachment/comp_doc_7july2018_final.pdf I looked through the numerous options of this function and, from my understanding, it doesn't seem that any of them give these values as an output. Thanks for taking the time to read this!
Sincerely, Jaclyn