akdemirlab/HiCPlotter

rao et al 2014 reproducing results

Opened this issue · 2 comments

Nohaosma commented

Dear Dr. kadir,
I am trying to plot the interaction matrices from Rao et al. 2014. the one you mentioned in your readme.
I am more interested in the interaction matrices which I downloaded from GSE63525. I downloaded the HMEC cell line.
whenever I try to convert the interaction matrices to a pivot matrix, it doesn't give me the anticipated results. I am not expert as you in programming so, please would you help me plot this file.

akdemirlab commented

Hi,
Are you looking for a specific chromosome? I can try to share that file with you so you can visualize the genomic location you are interested in.

Nohaosma commented

Thanks for your quick response.
I did download the HMEC interchromosomal matrices from GSE63525 and I want to plot each chromosome.
the matrices contain three column for the genomic positions and the count.
How can I convert these matrices to the same matrix you showed here (HMEC-chr10_25kb.RAWobserved_KRnormalizedMatrix.txt)