Project #13341
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#13341 : Serpentine: a flexible 2D binning method for differential Hi-C analysis
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Name of Applicant : Vittore Scolari
Date of application : 18-06-2019
Unit : Spatial Regulation of Genomes
Location : Jacob 4etage 26.04.05a
Phone : 8649
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Project context and summary :

Hi-C contact maps reflect the relative contact frequencies between pairs of genomic loci, quantified through deep-sequencing. Differential analyses of these maps facilitate downstream biological interpretations. However, the multi-fractal nature of the DNA polymer inside the cellular envelope results in frequency values spanning several orders of magnitude: contacts involving loci pairs at large genomic distance are much sparser compared to closer pairs. The same is true for poorly covered regions such as telomeres and repeated sequences. Poor coverage translates into low signal-to-noise ratios. There is no clear consensus to address this limitation. We present a fast, flexible procedure operating on simple data that takes into account 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.

Related team publications :
Characterizing meiotic chromosomes' structure and pairing using a designer sequence optimized for Hi‐C
Kinetic signature of cooperativity in the irreversible collapse of a polymer
Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle
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Project Type : Short
Status : Closed
Publication : 10.1093/bioinformatics/btaa249
Global Satisfaction for this application : Excellent (5/5)

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