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  • Undergraduate Student
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  • Visiting Scientist
  • Deputy Director of Center
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  • Deputy Head of Facility
  • Director of Center
  • Director of Department
  • Director of Institute
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Scientific Fields
Diseases
Organisms
Applications
Technique
Starting Date
21
Jul 2020
Status
Ongoing
Members
5
Structures
2

About

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320618/

Motivation: Hi-C contact maps reflect the relative contact frequencies between pairs of genomic loci, quantified through deep sequencing. Differential analyses of these maps enable downstream biological interpretations. However, the multi-fractal nature of the chromatin polymer inside the cellular envelope results in contact frequency values spanning several orders of magnitude: contacts between loci pairs separated by large genomic distances are much sparser than closer pairs. The same is true for poorly covered regions, such as repeated sequences. Both distant and poorly covered regions translate into low signal-to-noise ratios. There is no clear consensus to address this limitation.

Results: We present Serpentine, a fast, flexible procedure operating on raw data, which considers the contacts in each region of a contact map. Binning is performed only when necessary on noisy regions, preserving informative ones. This results in high-quality, low-noise contact maps that can be conveniently visualized for rigorous comparative analyses.

Availability and implementation: Serpentine is available on the PyPI repository and

https://github.com/koszullab/serpentine

documentation and tutorials are provided at

https://serpentine.readthedocs.io/en/latest/