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ma-compbio / SNIPER

nuclear compartments, subcompartments, nuclear organization, Hi-C, autoencoder
MIT License
29 stars 11 forks source link

can not download data #2

Open cquzys opened 5 years ago

cquzys commented 5 years ago

I can not download the data you given, and can you tell me what is the crop in you project?

kairukuma commented 5 years ago

Hello, are you trying to access the data from China? You may have to use a VPN to access Box if it's been blocked.

The crop here includes matrix rows and columns that were removed from the GM12878 inter-chromosomal Hi-C matrix as they were too sparse (greater than 30% of entries were zeros or undefined). The crop is important in running SNIPER because it ensures that the same rows and columns are removed from the Hi-C matrices of other cell types.

cquzys commented 4 years ago

Thanks for your share, and I have other questions that confuse me. Firstly, why you divide the chromosomes into odd and even to construct a matrix. Secondly, I find the number of loci in chromosome 22 of annotations file GM12787_track.bed does not match that in cropMap. the loci number in GM12787_track.bed is 322, but that in cropMap is 352(because of GM12787 coverage ?), in principle, they should are the same. Thirdly, how can I get the whole cropMap which is not divided into odd and even style