corner_score = the corner score, a score indicating the likelihood that a pixel is at the corner of a contact domain.color = the color that the feature will be rendered as if loaded in Juicebox.x1,x2/y1,y2 = the interval spanned by the domain (contact domains manifest as squares on the diagonal of a Hi-C matrix and as such: x1=y1, x2=y2).chromosome = the chromosome that the domain is located on.Passing in a value >0 will result in that value being used directly.Īrrowhead uses the following parameters if optional flags are not provided.Ĭhromosome1 x1 x2 chromosome2 y1 y2 colorĮxplanations of each field are as follows: Passing in a value of 0 will result in the jar calculating the number of available threads. As of Juicer Tools Version 1.13.02, the default number of threads used is 1. -threads Number of threads to use (Arrowhead is multi-threaded).Generally, KR (Knight-Ruiz) balancing should be used when available. -k Normalizations (case sensitive) that can be selected.
Generally, 5kB (5000) or 10kB (10000) resolution is used depending on the depth of sequencing in the HiC file(s).
: Feature list of loops/domains for which block scores are to be calculated.NOTE - If you want to find scores for a feature and control list, both must be provided: Can be visualized directly in Juicebox as a 2D annotation. : Final list of all contact domains found by Arrowhead.
Running Arrowhead on MAPQ>30 and MAPQ>0 files generally gives comprable results. This is the file you would load into Juicebox. : Address of HiC file which should end with ".hic".
0 kommentar(er)
