Transcriptome Completeness

Score transcriptome completeness from supplied ortholog classifications.

Description

Ortholog completeness summaries divide supplied classifications into complete, fragmented and missing shares.

Ortholog completeness summaries divide supplied classifications into complete, fragmented and missing shares. Searching for orthologs is a separate upstream task.^[1]

Score transcriptome completeness from supplied ortholog classifications.

When to use Transcriptome Completeness

Use this tool to score transcriptome completeness from supplied ortholog classifications.

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 Transcriptome Completeness 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 completeOrthologs, fragmentedOrthologs, missingOrthologs, minimumCompletePercent using the field table and calculation rules, then run the tool.
Read completePercent, fragmentedPercent, missingPercent, passes. 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
completeOrthologs	Complete orthologs	number	Required
fragmentedOrthologs	Fragmented orthologs	number	Required
missingOrthologs	Missing orthologs	number	Required
minimumCompletePercent	Minimum complete percent	number	Required

Supply nonnegative category counts with a positive combined total and a minimum complete percentage. Return all three percentages and an inclusive completeness flag.

complete%=100 complete/(complete+fragmented+missing)

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

Output field	Meaning	Value type
completePercent	Complete percent	number
fragmentedPercent	Fragmented percent	number
missingPercent	Missing percent	number
passes	Passes	boolean

json

{
  "input": {
    "completeOrthologs": 80,
    "fragmentedOrthologs": 10,
    "missingOrthologs": 10,
    "minimumCompletePercent": 75
  },
  "output": {
    "completePercent": 80,
    "fragmentedPercent": 10,
    "missingPercent": 10,
    "passes": true
  }
}

Limitations and assumptions

The categories must be mutually exclusive and use the same reference set. Counts need not be integers in the runtime, and no BUSCO search, lineage selection or assembly validation is executed.

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 Utr Length Ratio: Compare 3-prime and 5-prime UTR lengths. For a complementary task, use Junction Annotation Tally: Tally annotated versus novel observed splice junctions.

References

Transcriptome Completeness — tool.io

Similar or alternative tools

Utr Length Ratio
Compare 3-prime and 5-prime UTR lengths.
Junction Annotation Tally
Tally annotated versus novel observed splice junctions.