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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