![]() ![]() The segment in the “highlighting window” is highlighted in yellow. In addition, users can directly input the genomic region of interest in the “viewing window” text box, and highlight any part of such genomic region using the “highlighting window” text box. For example, clicking “2x” button reduces the viewing window to half of the current range, while clicking “-10x” button increases the viewing window to ten times of the current range. The zoom buttons control the range of the viewing window. Clicking the one arrow (“”) buttons moves the window 10% in the specified direction, while clicking the double arrow (“>”) buttons moves the window 25% in the specified direction. Specially, the arrow buttons control which direction the viewing window moves. ![]() The second section includes the “move” and “zoom” buttons, which allow users to visualize genomic regions of interest at desired resolutions. The primary goal of HUGIn is to identify the target gene(s) of SNP(s) or region(s) of interest, as in contrast to pinpointing THE causal SNP(s). Given the experimental protocol (for example, using 4 base pair or 6 base pair restriction enzyme) and typical sequencing depth of Hi-C experiments (for example, Schmitt et al generated an average of ~214 million raw reads per tissue, and an average of ~809 million raw reads per cell line), we cannot achieve the base pair resolution of chromatin interactions. Note that 40Kb is the resolution of the Hi-C data for the 7 cell lines and 14 primary tissues generated by Schmitt et al 2016. Internally, HUGIn identifies the 40Kb bin containing the Anchor Position user specifies. For both plots, the bin containing the Anchor Position is highlighted in gray. After typing in the Anchor Position, users can click the “RUN” button (in red) to generate the virtual 4C plot (by default), as well as a more compact heatmap plot (available when clicking on the Information Type box). Accepted Anchor Position includes SNP names in rs nomenclature (dbSNP version 147), chr:bp (e.g., the default chr5:53,298,025), and multiple gene IDs including the common name, RefSeq gene name, ensemble ID, and UCSC gene name. By default, this Anchor Position is set to chr5:53,298,025, which is the position of SNP rs6450176, associated with type 2 diabetes status and adiponectin level. In the GWAS context, this Anchor Position is mostly defined by a SNP ID. The first section is the “Anchor Position”, which defines the anchor of long range chromatin interactions. The main interface of HUGIn consists of the following four major sections (Figure 1 below). ![]() HUGIn hosts a compendium of Hi-C data (Schmitt et al., 2016) mapped to the human reference genome hg19. User Tutorial User Interface Output Extracting Figures FAQs Back to Main Pageįor questions or comments about HUGIn, please contact jsmartin at. Downloadsĭownload the latest version of GIMP 2.HUGIn is designed to explore chromatin organizations across multiple human cell lines and primary tissues. This tutorial is great for amateur or professional photographers that need to stitch together multiple images. I prefer the Hugin method as I think it produces a better result in less time. In this GIMP 2.10.2 tutorial, I show you how to stitch together multiple images to create one panoramic image! I’ll show you two methods, one involving Hugin and the other involving Pandora. Stitch Panoramic Images in GIMP 2.10.2 (Two Methods) ![]()
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