#Juicebox youtube how to#

Below, hover text shows additional data for one of the highlighted peaks. At the top right, a mini-map shows the whole chromosome at low resolution. A peak in the CTCF track, indicating CTCF binding, is seen at most loop anchors. Several peaks are annotated (cyan), each peak indicating the presence of a chromatin loop. Two-dimensional features can be superimposed on the main map. Users can load one-dimensional tracks and compare them to features seen in the heatmap. The toolbar at the top allows users to quickly navigate between different chromosomes, views, normalizations, and resolutions. Here, we see a screenshot of Juicebox zoomed into 5-Kb resolution on chromosome 3. Juicebox enables exploration of contact maps at many resolutions Juicebox was an invaluable tool in making biological discoveries across many size scales in our groupвЂ™s recent paper ( Rao et al., 2014). Users can create their own heatmaps to explore their own experiments ( Durand et al., 2016). Multiple maps can be browsed side by side simultaneously and compared with one another in various ways, revealing both conservation and variation across cell types and species. Individual maps can be normalized (corrected for experimental bias), compared to one-dimensional (1D) tracks (such as gene tracks or chromatin immunoprecipitation sequencing data), and compared to 2D feature lists (such as loop and domain annotations). Juicebox allows users to explore Hi-C heatmaps interactively, zooming in and out just as a user of Google Earth might zoom in and out of a geographic map it integrates many technologies developed for the Integrative Genomics Viewer ( Robinson et al., 2011) with a broad ensemble of methods specifically designed for handling 2D contact data. Here we introduce Juicebox, a tool for exploring Hi-C data and contact maps in general ( Figure 1). Also, most of these systems are designed to show specific, previously published datasets, and they do not allow users to visualize their own experiments. Users cannot zoom in and out in real time. Like a paper atlas, these browsers show the map at a single resolution (typically either 1-Mb or 100-Kb), either in its entirety ( Servant et al., 2012 Paulsen et al., 2014 Lieberman-Aiden et al., 2009) or very close to the diagonal ( Zhou et al., 2013).

Several Hi-C visualization systems exist. At coarser resolutions, more of the map can be shown, but the fine structure can no longer be resolved. At the highest meaningful resolutions, published Hi-C heatmaps contain trillions of entries, and only a tiny portion can be displayed at any given time. Typically, the pairwise interactions produced by Hi-C experiments are visualized as a heatmap: the linear genome is partitioned into loci of a fixed size, or resolution (e.g., 1-Mb or 1-Kb) and each entry in the two-dimensional (2D) heatmap corresponds to the number of contacts observed between a pair of loci during the experiment.Дeveloping adequate visualizations for Hi-C heatmaps is a challenge, because the size of the meaningful biological features they contain ranges over at least seven orders of magnitude: from loops anchored at 20-bp CTCF sites to territories that extend across 200-Mb chromosomes. This results in a Hi-C contact map: a list of pairs of genomic positions that were adjacent to each other in three-dimensional (3D) space. In Hi-C, DNA loci that are spatially proximate in a system of interest (such as a cell nucleus or an in vitro DNA preparation) are ligated to one another and sequenced.

вЂЌ Additional Configurations: Set configurations such as the rules for how changes can be made to your project, the discount rate, and the bonding curve rate.Hi-C is a widely employed method for studying how genomes are folded in three dimensions ( Rao et al., 2014).

You can also set the percentage of tokens that will be reserved for the project owners.

Reserved tokens: Reward community members with your projectвЂ™s tokens when they contribute to the fundraiser.

The platform allows you to commit portions of every withdrawal to other Etherum wallets or Juicebox projects, which you can use to pay contributors, charities, other projects, or anyone else.

Distribution: Define how you will distribute your funds.

You can also set the duration and frequency (recurring or one-time) of your funding cycles.

#Juicebox youtube how to#

You have the option to set a funding target and decide how to redistribute surplus revenue to your community. Funding: Define how your project will earn and manage funds.Appearance: Choose your design including project name, handle, links, and other details.Through its platform, you can configure and deploy a smart contract that allows you to manage fundraising and token distribution for your project.