Insert Size Mode

Find the modal insert size, breaking ties toward the shorter fragment.

Description

The modal insert size is the most frequently observed size.

The modal insert size is the most frequently observed size. A deterministic tie rule keeps a multi-modal sample's reported single value reproducible.^[1]

Find the modal insert size, breaking ties toward the shorter fragment.

When to use Insert Size Mode

Use this tool to find the modal insert size, breaking ties toward the shorter fragment.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use Insert Size Mode and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter insertSizesBp using the field table and calculation rules, then run the tool.
Read modeBp, modeCount, uniqueInsertSizes. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
insertSizesBp	Insert sizes bp	list of number	Required

Enter a nonempty list of nonnegative safe-integer sizes in bp. Tally exact sizes, order by decreasing count and then increasing size, and return mode, its count and number of distinct sizes. Zero is accepted as a supplied size.

mode=highest-frequency size, then shortest size on ties

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
modeBp	Mode bp	number
modeCount	Mode count	number
uniqueInsertSizes	Unique insert sizes	number

json

{
  "input": {
    "insertSizesBp": [
      100,
      200,
      200,
      300
    ]
  },
  "output": {
    "modeBp": 200,
    "modeCount": 2,
    "uniqueInsertSizes": 3
  }
}

Limitations and assumptions

No histogram smoothing, alignment parsing or fragment-quality interpretation is performed. Reporting one mode can hide other peaks or broad distributions.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Library Complexity: Measure duplicate fraction and library complexity from distinct fragments. For a complementary task, use DV200 Fragment Quality: Calculate the share of RNA fragments longer than a user-selected cutoff.

References

Insert Size Mode — tool.io

Similar or alternative tools

Library Complexity
Measure duplicate fraction and library complexity from distinct fragments.
DV200 Fragment Quality
Calculate the share of RNA fragments longer than a user-selected cutoff.