Thanks for the tools, work really well so far. Just one point that caused quite some confusion. The manual for the normalization step says:
--setToZeroThreshold
"It is recommended to set it for the normalize mode “smallest” to 1.0."
I did so and observed that the smallest sample was very different from the rest by having much more inter-chromosomal interactions. I guess that choosing exactly 1.0 deletes most inter-chromosomal interactions in all samples except for the smallest. Hence, I wouldn't recommend choosing 1.0 and I would also think about disabling this threshold in the "smallest" mode.
Hi there
Thanks for the tools, work really well so far. Just one point that caused quite some confusion. The manual for the normalization step says:
--setToZeroThreshold
"It is recommended to set it for the normalize mode “smallest” to 1.0."
I did so and observed that the smallest sample was very different from the rest by having much more inter-chromosomal interactions. I guess that choosing exactly 1.0 deletes most inter-chromosomal interactions in all samples except for the smallest. Hence, I wouldn't recommend choosing 1.0 and I would also think about disabling this threshold in the "smallest" mode.
Best,
Marc