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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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sparseToDense.py error #557

Open aaannaw opened 1 year ago

aaannaw commented 1 year ago

Hi When I use sparseToDense.py to convert HiC-Pro output into dense format: python 00.sparseToDense.py -b Ma_40000_abs.bed Ma_40000_iced.matrix --perchr. The first row and column of the output result of Chr1 (Ma_40000_iced_Chr1_dense.matrix) are both zero. Is it normal?The pictures of My bed file (Ma_40000_abs.bed) , matrix file (Ma_40000_iced.matrix) and the output file of sparseToDense.py( 00.Ma_40000_iced_Chr1_dense.matrix) are as follows. image image image Could you give me any suggestion? Looking forward with your reply!

songxh1996 commented 1 year ago

Hi When I use sparseToDense.py to convert HiC-Pro output into dense format: python 00.sparseToDense.py -b Ma_40000_abs.bed Ma_40000_iced.matrix --perchr. The first row and column of the output result of Chr1 (Ma_40000_iced_Chr1_dense.matrix) are both zero. Is it normal?The pictures of My bed file (Ma_40000_abs.bed) , matrix file (Ma_40000_iced.matrix) and the output file of sparseToDense.py( 00.Ma_40000_iced_Chr1_dense.matrix) are as follows. image image image Could you give me any suggestion? Looking forward with your reply!

I got the same result as yours, is your problem solved

Miracle-Yao commented 3 months ago

Hi, @songxh1996 @aaannaw

It does happen that the output densematrix is always shifted down and to the right by one resolution, with or without the --perchr parameter. Is there a follow up to this issue?