Strand Specificity

Check library strandedness using sense-versus-antisense reads.

Description

Strand specificity compares assigned sense and antisense reads under a chosen annotation convention.

Strand specificity compares assigned sense and antisense reads under a chosen annotation convention. A sense percentage remains defined when no antisense reads occur, while an ordinary ratio does not.^[1]

Check library strandedness using sense-versus-antisense reads.

When to use Strand Specificity

Use this tool to check library strandedness using sense-versus-antisense reads.

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 Strand Specificity 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 senseReads, antisenseReads, minimumSensePercent using the field table and calculation rules, then run the tool.
Read sensePercent, senseAntisenseRatio, strandSpecific. 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
senseReads	Sense reads	number	Required
antisenseReads	Antisense reads	number	Required
minimumSensePercent	Minimum sense percent	number	Required

Enter nonnegative sense/antisense counts with a positive total and a finite minimum sense percentage. Return percentage and inclusive specificity flag. When antisense is zero, the ratio output is the sense count as a finite fallback, not infinity.

sense%=100 sense/(sense+antisense); ratio=sense/antisense unless antisense=0

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

Output field	Meaning	Value type
sensePercent	Sense percent	number
senseAntisenseRatio	Sense antisense ratio	number
strandSpecific	Strand specific	boolean

json

{
  "input": {
    "senseReads": 80,
    "antisenseReads": 20,
    "minimumSensePercent": 75
  },
  "output": {
    "sensePercent": 80,
    "senseAntisenseRatio": 4,
    "strandSpecific": true
  }
}

Limitations and assumptions

No alignment, annotation or protocol-orientation determination is performed. Threshold bounds are not separately enforced, and the zero-denominator fallback should not be read as an ordinary ratio.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use Canonical Splice Support: Count canonical GT–AG splice junction motifs. For a complementary task, use Multimapper Fraction: Measure ambiguous multi-mapper assignment share.

References

Strand Specificity — tool.io

Similar or alternative tools

Canonical Splice Support
Count canonical GT–AG splice junction motifs.
Multimapper Fraction
Measure ambiguous multi-mapper assignment share.