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

File String 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:

Field	Description
`A`	Column vector containing intensity of A fluorescence tag
`C`	Column vector containing intensity of C fluorescence tag
`G`	Column vector containing intensity of G fluorescence tag
`T`	Column 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:

Field	Description
`peak_index`	Column vector containing the position in the SCF file for the start of the data for each peak
`prob_A`	Column vector containing the probability of each base in the sequence being an A
`prob_C`	Column vector containing the probability of each base in the sequence being a C
`prob_G`	Column vector containing the probability of each base in the sequence being a G
`prob_T`	Column vector containing the probability of each base in the sequence being a T
`base`	Column 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. For more information on SCF files, see

http://www.mrc-lmb.cam.ac.uk/pubseq/manual/formats_unix_2.html

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

scfread - Read trace data from SCF file

Syntax

Arguments

Description

Examples

See Also

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