scfread

Read trace data from SCF file

Syntax

Sample = scfread(File)
[Sample, Probability] = scfread(File)
[Sample, Probability, Comments] = scfread(File)
[A, C, G, T] = scfread (File)
[A, C, G, T, ProbA, ProbC, ProbG, ProbT] = scfread (File)
[A, C, G, T, ProbA, ProbC, ProbG, ProbT, Comments, PkIndex, Base] = scfread (File)

Arguments

FileString specifying the file name or a path and file name of an SCF formatted file.

Description

scfread reads data from an SCF formatted file into MATLAB® structures.

Sample = scfread(File) reads an SCF formatted file and returns the sample data in the structure Sample, which contains the following fields:

FieldDescription
AColumn vector containing intensity of A fluorescence tag
CColumn vector containing intensity of C fluorescence tag
GColumn vector containing intensity of G fluorescence tag
TColumn vector containing intensity of T fluorescence tag

[Sample, Probability] = scfread(File) also returns the probability data in the structure Probability, which contains the following fields:

FieldDescription
peak_indexColumn vector containing the position in the SCF file for the start of the data for each peak
prob_AColumn vector containing the probability of each base in the sequence being an A
prob_CColumn vector containing the probability of each base in the sequence being a C
prob_GColumn vector containing the probability of each base in the sequence being a G
prob_TColumn vector containing the probability of each base in the sequence being a T
baseColumn vector containing the called bases for the sequence

[Sample, Probability, Comments] = scfread(File) also returns the comment information from the SCF file in a character array Comments.

[A, C, G, T] = scfread (File) returns the sample data for the four bases in separate variables.

[A, C, G, T, ProbA, ProbC, ProbG, ProbT] = scfread (File) also returns the probabilities data for the four bases in separate variables.

[A, C, G, T, ProbA, ProbC, ProbG, ProbT, Comments, PkIndex, Base] = scfread (File) also returns the peak indices and called bases in separate variables.

SCF files store data from DNA sequencing instruments. Each file includes sample data, sequence information, and the relative probabilities of each of the four bases.

Examples

[sampleStruct, probStruct, Comments] = scfread('sample.scf')
sampleStruct = 

    A: [10827x1 double]
    C: [10827x1 double]
    G: [10827x1 double]
    T: [10827x1 double]


probStruct = 

    peak_index: [742x1 double]
        prob_A: [742x1 double]
        prob_C: [742x1 double]
        prob_G: [742x1 double]
        prob_T: [742x1 double]
          base: [742x1 char]


Comments =

SIGN=A=121,C=103,G=119,T=82
SPAC= 16.25
PRIM=0
MACH=Arkansas_SN312
DYEP=DT3700POP5{BD}v2.mob
NAME=HCIUP1D61207
LANE=6
GELN=
PROC=
RTRK=
CONV=phred version=0.990722.h
COMM=
SRCE=ABI 373A or 377 
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