CIGAR Junction Positions

Extract zero-based half-open reference skip junctions from CIGAR N operations.

Description

CIGAR N operations describe reference skips, commonly associated with RNA splice junctions.

CIGAR N operations describe reference skips, commonly associated with RNA splice junctions. Reference-consuming operations determine each skip’s boundaries.^[1]

Extract zero-based half-open reference skip junctions from CIGAR N operations.

When to use CIGAR Junction Positions

Use this for the following task: Extract zero-based half-open reference skip junctions from CIGAR N operations.

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.

How to use CIGAR Junction Positions and understand its results

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
Enter cigar, alignmentStart using the field table, then run the tool.
Read junctionStarts, junctionEnds, junctionCount. Interpret flags, units, ordering and placeholder values using the rules below.
Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.

Input field	Meaning	Value type and bounds	Requirement
cigar	CIGAR	string; minimum text length 2; maximum text length 1000000; pattern ^(?:[1-9][0-9]*[MIDNSHP=X])+(?![\s\S])	Required
alignmentStart	Zero-based reference start; subtract one from a mapped SAM POS.	integer; minimum 0	Required

Start at the supplied zero-based position. Advance for M,D,N,=,X and record every N before advancing; I,S,H,P do not advance reference position.^[2]

junction = [currentReferencePosition,currentReferencePosition+Nlength)

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
junctionStarts	Junction starts	list of integer
junctionEnds	Junction ends	list of integer
junctionCount	Junction count	integer

json

{
  "input": {
    "cigar": "10M20N5M",
    "alignmentStart": 100
  },
  "output": {
    "junctionStarts": [
      110
    ],
    "junctionEnds": [
      130
    ],
    "junctionCount": 1
  }
}

Limitations and assumptions

SAM POS is 1 based and needs conversion before use here. The tool reports skips without establishing biological splice events.

The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.

Alternative or Complementary methods

Choose CIGAR Operation Summary for this operation: Summarize CIGAR operations and distinguish query-consuming and reference-consuming bases. For a complementary task, use Gene Model Junction Support for this operation: Validate exon-model introns against coordinate-matched observed junction read evidence.

Further background: Background specification: CIGAR Junction Positions.

References

Background specification: CIGAR Junction Positions — GA4GH / HTS specifications
CIGAR Junction Positions — tool.io

Similar or alternative tools

CIGAR Operation Summary
Summarize CIGAR operations and distinguish query-consuming and reference-consuming bases.
Gene Model Junction Support
Validate exon-model introns against coordinate-matched observed junction read evidence.