Number_collapsed centroid1 centroid2 radius See this Colab notebook with an example run: notebookĬhromosome1 x1 x2 chromosome2 y1 y2 color observedĮxpected_bottom_left expected_donut expected_horizontal expected_verticalįdr_bottom_left fdr_donut fdr_horizontal fdr_vertical Passing in a value >0 will result in that value being used directly. 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 (HiCCUPS is multi-threaded). (e.g "-r 5000,10000 -d 20000,21000” would merge pixels within 20kB of each other at 5kB resolution and within 21kB at 10kB resolution. Different distances can be used for each resolution using commas. d Distances used for merging nearby pixels to a centroid. These thresholds (in order) represent: > threshold allowed for sum of FDR values of the horizontal, vertical, donut, and bottom left filters (an accepted loop must stay below this threshold) > threshold ratio that both the horizontal and vertical filters must exceed > threshold ratio that both the donut and bottom left filters must exceed > threshold ratio that at least one of the donut and bottom left filters must exceed Four values must be given, separated by commas (e.g. t Thresholds for merging loop lists of different resolutions. (e.g "-r 5000,10000 -p 10,6" would run at window width 10 for resolution 5000 and window width 6 for resolution 10000) Different window widths can be used for each resolution using commas. i Window width used for finding enriched pixels in HiCCUPS. (e.g "-r 5000,10000 -p 4,2" would run at peak width 4 for resolution 5000 and peak width 2 for resolution 10000) Different peak widths can be used for each resolution using commas. p Peak width used for finding enriched pixels in HiCCUPS. Different FDR values can be used for each resolution using commas. f FDR values actually corresponding to max_q_val (i.e. Generally, KR (Knight-Ruiz) balancing should be used when available. k Normalizations (case sensitive) that can be selected. 50kB or 100kB) IMPORTANT: if multiple resolutions are used, the flags below can be configured so that different parameters are used for the different resolutions. Due to the nature of DNA looping, it is unlikely that loops will be found at lower resolutions (i.e. Multiple resolutions can be specified using commas (e.g. r Resolution(s) for which HiCCUPS will be run. Multiple chromosomes can be specified using commas (e.g. The number/letter for the chromosome can be used with or without appending the "chr" string. c Chromosome(s) on which HiCCUPS will be run. Larger values (with a dedicated GPU) will run fastest. Matrix size will not effect the result, merely the time it takes for hiccups. Integrated GPUs are unlikely to run sizes larger than 90 or 100. Dedicated GPUs should be able to use values such as 500, 1000, or 2048 without trouble. m Maximum size of the submatrix within the chromosome passed on to GPU (Must be an even number greater than 40 to prevent issues from running the CUDA kernel). CPU version only searches near the diagonal (in order to run in a reasonable amount of time), so it will not include regions far from the diagonal. This will create additional files in addition to the ones created in prior versions. Starting with version 1.12.03, the given pixels are post-processed at each resolution and the results are merged across resolutions. HiCCUPS will then return enrichments for these specified loops for each resolution. Specified_loop_list is an optional positional argument which should point to a Juicebox formatted loop list. Intermediate files created by HiCCUPS (raw pixels from GPU, clustered pixels for each resolution, and FDR thresholds) will also be saved in this directory. These can be disabled using the suppress flag below. By default, various values critical to the HICCUPS algorithm are saved as attributes for each loop found. Can be visualized directly in Juicebox as a 2D annotation. : Directory containing final merged list of all loops found by HiCCUPS.HiCCUPS should be run using MAPQ>30 hic files. This is the file you will load into Juicebox.
: Address of HiC file which should end with ".hic".
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