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sshen82 / BandNorm

Simple Normalization Method for single-cell Hi-C
GNU General Public License v3.0
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Input format #4

Closed randel closed 2 years ago

randel commented 2 years ago

Hi Siqi,

Thanks for the nice package! I have a question regarding the input format below.

chr1 0 chr1 10000 9 chr1 10000 chr1 10000 20

My input is from HiCcompare::cooler2bedpe and listed below. It has seven columns instead of five. Can you let me know which start/end matches to your bin column?

chr1 start1 end1 chr2 start2 end2 IF chr1 220000 230000 chr1 220000 230000 2 chr1 510000 520000 chr1 510000 520000 3

For scGAD, do you only consider cis contact or both cis and trans? Thanks!

sshen82 commented 2 years ago

Hi, Thank you for using the package!

Our package is 0-indexed, so the correct input is chr1 start1 chr2 start2 IF.

For scGAD, currently our method only considers cis contact.

Yours sincerely, Siqi Shen