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tanlongzhi / dip-c

Tools to analyze Dip-C (or other 3C/Hi-C) data
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Using align.py #38

Closed tarak77 closed 4 years ago

tarak77 commented 4 years ago

Hey @tanlongzhi , How would one use the align.py script? What all inputs can we give and what outputs can we get? Is it possible to get a genome wide RMSD score?

Thanks!

tanlongzhi commented 4 years ago

Hey @tarak77, the align functionality can be used as following:

dip-c align -o aligned. a.3dg b.3dg. c.3dg

The inputs are any numbers of .3dg files. In the above example, we input 3 files (0th: a.3dg, 1st:b.3dg, 2nd: c.3dg). There're two outputs:

  1. The standard error gives RMSD values between each pair of inputs (in this case, 3 pairs), and an overall RMSD value (shown following RMS RMSD:, which is the r.m.s. of all RMSDs). Note that RMSDs are only calculated for particles common to all input files.
  2. Each input file is also aligned to each other input file. In the above example, one such output file, aligned.0_to_2.3dg, is the result of aligning the 0th input file (a.3dg) to the 2nd input file (c.3dg). Note that each output file contains all particles in original input file, even if some are not present in the input file that it aligns to.
tarak77 commented 4 years ago

Ok I see. thanks