ecl-logo Documentation

Object[Analysis, DNASequencing]

Base calling analysis for assigning nucleobase sequences to DNA-sequencing data.

Organizational Information

    Name

    Name of this Object.
    Format: Single
    Class: String
    Programmatic Pattern: _String
    Pattern Description: A string.

    ID

    ID of this Object.
    Format: Single
    Class: String
    Programmatic Pattern: _String
    Pattern Description: The ID of this object.

    Object

    Object of this Object.
    Format: Single
    Class: Expression
    Programmatic Pattern: Object[Analysis, DNASequencing, _String]
    Pattern Description: The object reference of this object.

    Type

    Type of this Object.
    Format: Single
    Class: Expression
    Programmatic Pattern: Object[Analysis, DNASequencing]
    Pattern Description: Object[Analysis, DNASequencing]

    Notebook

    Notebook this object belongs to.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Pattern Description: An object of that matches ObjectP[Object[LaboratoryNotebook]].
    Relation: Object[LaboratoryNotebook][Objects]

    Author

    The person who ran the analysis.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Relation: Object[User]

General

Analysis & Reports

    SequenceAssignment

    The sequence of nucleobases assigned to input data by this DNA sequencing analysis.
    Format: Single
    Class: String
    Programmatic Pattern: _String

    SequenceBases

    A sequential list of the individual bases assigned to input data by this DNA sequencing analysis.
    Format: Multiple
    Class: String
    Programmatic Pattern: A | T | C | G | N

    QualityValues

    For each member of SequenceBases, the quality value of the base assignment. A quality value of >20 is considered an accurate base assignment; a quality value between 15-19 is considered a mediocre accuracy; a quality value below 15 is considered poor accuracy.
    Format: Multiple
    Class: Integer
    Programmatic Pattern: _Integer

    BaseProbabilities

    For each member of SequenceBases, the individual likelihood that each DNA nucleobase corresponds to that base.
    Format: Multiple

    [[1]] A

      Header: A
      Class: Real
      Programmatic Pattern: RangeP[0., 1.]

    [[2]] T

      Header: T
      Class: Real
      Programmatic Pattern: RangeP[0., 1.]

    [[3]] C

      Header: C
      Class: Real
      Programmatic Pattern: RangeP[0., 1.]

    [[4]] G

      Header: G
      Class: Real
      Programmatic Pattern: RangeP[0., 1.]

    SequencePeakPositions

    For each member of SequenceBases, the cycle read in the input electropherograms at which the base call was assigned.
    Format: Multiple
    Class: Real
    Programmatic Pattern: GreaterP[0.]

    UntrimmedSequenceBases

    A sequential list of the individual bases assigned to input data prior to sequence trimming.
    Format: Multiple
    Class: String
    Programmatic Pattern: A | T | C | G | N

    UntrimmedQualityValues

    For each member of UntrimmedSequenceBases, the quality value of the base assignment.
    Format: Multiple
    Class: Integer
    Programmatic Pattern: _Integer

    UntrimmedBaseProbabilities

    For each member of UntrimmedSequenceBases, the individual likelihood that each DNA nucleobase corresponds to that base.
    Format: Multiple

    [[1]] A

      Header: A
      Class: Real
      Programmatic Pattern: RangeP[0., 1.]

    [[2]] T

      Header: T
      Class: Real
      Programmatic Pattern: RangeP[0., 1.]

    [[3]] C

      Header: C
      Class: Real
      Programmatic Pattern: RangeP[0., 1.]

    [[4]] G

      Header: G
      Class: Real
      Programmatic Pattern: RangeP[0., 1.]

    UntrimmedSequencePeak Positions

    For each member of UntrimmedSequenceBases, the cycle read in the input electropherograms at which the base call was assigned.
    Format: Multiple
    Class: Real
    Programmatic Pattern: GreaterP[0.]

    PhredQualityParameters

    For each member of UntrimmedSequenceBases, the four-parameter Phred quality parameters (spacing, 7peak, 3peak, resolution) for that base. Used to calculate quality values and train quality value models.
    Format: Multiple
    Class: Compressed
    Programmatic Pattern: {NumericP, NumericP, NumericP, NumericP}

    SequencingElectropherogram TraceA

    The unitless raw electropherogram data corresponding to the nucleobase "A" used in this DNA sequencing analysis.
    Format: Single
    Class: Compressed
    Programmatic Pattern: CoordinatesP

    SequencingElectropherogram TraceC

    The unitless raw electropherogram data corresponding to the nucleobase "C" used in this DNA sequencing analysis.
    Format: Single
    Class: Compressed
    Programmatic Pattern: CoordinatesP

    SequencingElectropherogram TraceG

    The unitless raw electropherogram data corresponding to the nucleobase "G" used in this DNA sequencing analysis.
    Format: Single
    Class: Compressed
    Programmatic Pattern: CoordinatesP

    SequencingElectropherogram TraceT

    The unitless raw electropherogram data corresponding to the nucleobase "T" used in this DNA sequencing analysis.
    Format: Single
    Class: Compressed
    Programmatic Pattern: CoordinatesP
Last modified on Mon 26 Sep 2022 15:43:43
EMERALD CLOUD LAB
15500 Wells Port Drive
Austin, TX 78728
© 2023 Emerald Cloud Lab, Inc.