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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Read data to HiTC #436

Closed zji90 closed 3 years ago

zji90 commented 3 years ago

Hi,

I am very new to Hi-C analysis and sorry if the question is dumb. I got the output from HiC-pro and would like to read into HiTC for further analysis. I think I should use importC but I am not sure what files I should use as input arguments (con, xgi.bed, ygi.bed). I guess con should be something like iced/20000/20000_iced.matrix, right?

Also I see that under iced folder there are multiple subfolders 20000, 40000,150000, .... I wonder which one should I use?

Thanks!

BenxiaHu commented 3 years ago

it depends on which resolution you want. what do you want to do when you read Hi-C contact matrix using HiTC?

jiangpuxuan commented 2 years ago

Hello, I am also new to Hi-C. I download a zebrafish genome and finish the Hic-pro pipeline. Finally I found that there are too may strange chromosomes in my iced.matrix, appeared like "chr1_KZ115012v1_alt", etc.

It is known that zebrafish only have 25 chromosome. So I want to know the meaning of "chr1_KZ115012v1_alt".

Thank you for your help!

nservant commented 2 years ago

Hi, Look at your reference genome. Basically, you should have the 'canonical' chromosomes chr1, 2, 3... + many scaffolds or haplotypes which are not well assembled and appear in the reference as "chr*_alt". You can remove them from your reference genome if you only want to focus on the canonical chromosomes. Best