Filterscan Report

Filterscan Report: Fields

Name	Data Type
Sample	str
Branches	dict[str, str]
Reference	str
Region	str
Make each tile this length (if 0, use 2x the median read length)	int
Make adjacent tiles overlap by at least this fraction of length	float
Erase the filter reports/batches from the tiling step	bool
Find correlated pairs at this false discovery rate (FDR)	float
Cluster only the regions with at least this many correlated pairs	int
Among pairs that survive the endpoint-peak filter, drop any pair whose L1 (Manhattan) distance to its nearest surviving neighbor exceeds this percentile of all such distances. Pairs more isolated than this threshold are treated as noise.	float
When testing whether a position is a significant hub of correlated pair endpoints, aggregate counts over a window of this many adjacent positions: forward (pos5, pos5+1, …, pos5+window) for 5’ ends, backward (pos3-window, …, pos3) for 3’ ends. Larger values boost statistical power for helices whose endpoints are not always at exactly the same position.	int
Minimum number of other surviving pairs that must lie within the pair-distance-percentile L1 threshold for a pair to be kept. Setting this above 1 filters out small coincidental clusters of noise pairs (‘buddy noise’) at the cost of potentially clipping domain edges.	int
Cluster only the regions with at least this many positions	int
Cluster only the regions with no more than this many positions	int
If there are gaps between regions to cluster, OMIT (do not cluster) the gaps, INSERT a new region into each gap, or EXPAND the existing regions to fill the gaps	str
Coordinates of tiles (end5, end3)	list[list[int]]
Number of significant pairs detected	int
Number of domains detected	int
Coordinates of domains (end5, end3)	list[list[int]]
Time began	str
Time ended	str
Time taken (minutes)	float
Version of SEISMIC-RNA	str

Filterscan Report: Example

{
    "Sample": "sample1",
    "Branches": {
        "idmut": "",
        "filterscan": ""
    },
    "Reference": "myref",
    "Region": "full",
    "Make each tile this length (if 0, use 2x the median read length)": 0,
    "Make adjacent tiles overlap by at least this fraction of length": 0.5,
    "Erase the filter reports/batches from the tiling step": true,
    "Find correlated pairs at this false discovery rate (FDR)": 0.05,
    "Cluster only the regions with at least this many correlated pairs": 2,
    "Among pairs that survive the endpoint-peak filter, drop any pair whose L1 (Manhattan) distance to its nearest surviving neighbor exceeds this percentile of all such distances. Pairs more isolated than this threshold are treated as noise.": 95.0,
    "When testing whether a position is a significant hub of correlated pair endpoints, aggregate counts over a window of this many adjacent positions: forward (pos5, pos5+1, ..., pos5+window) for 5' ends, backward (pos3-window, ..., pos3) for 3' ends. Larger values boost statistical power for helices whose endpoints are not always at exactly the same position.": 2,
    "Minimum number of other surviving pairs that must lie within the pair-distance-percentile L1 threshold for a pair to be kept. Setting this above 1 filters out small coincidental clusters of noise pairs ('buddy noise') at the cost of potentially clipping domain edges.": 2,
    "Cluster only the regions with at least this many positions": 20,
    "Cluster only the regions with no more than this many positions": 1200,
    "If there are gaps between regions to cluster, OMIT (do not cluster) the gaps, INSERT a new region into each gap, or EXPAND the existing regions to fill the gaps": "omit",
    "Coordinates of tiles (end5, end3)": [
        [
            1,
            180
        ]
    ],
    "Number of significant pairs detected": 363,
    "Number of domains detected": 2,
    "Coordinates of domains (end5, end3)": [
        [
            3,
            56
        ],
        [
            124,
            174
        ]
    ],
    "Time began": "2026-07-02 at 10:07:22",
    "Time ended": "2026-07-02 at 10:07:48",
    "Time taken (minutes)": 0.44,
    "Version of SEISMIC-RNA": "0.26.0dev"
}