| Bioinformatics Toolbox | |
Read trace data from SCF file
[Sample, Probability, Comments] = scfread('File')
[A,C,T,G, ProbA, ProbC, ProbG, ProbT,
Comments] = scfread ('File')
File | SCF formatted file. Enter a filename or a path and filename. |
scfread reads data from a SCF formatted file into a MATLAB structure.
[Sample, Probability, Comments] = scfread('File') reads an SCF formatted file and returns the sample data in the structure Sample, with fields A, C, T, G, probability data in the structure Probability, and comment information from the file in Comments.
[A,C,T,G, ProbA, ProbC, ProbG, ProbT, Comments] = scfread ('File') reads an SCF formatted file and returns the sample data and probabilities for nucleotides 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 of SCF files can be found at
ftp://ftp.ncbi.nih.gov/pub/TraceDB/example/
Unzip the file bcm-example.tgz with SCF files to your MATLAB working directory.
[Sample, Probability, Comments] = scfread('HCIUP1D61207.scf')
Sample =
A: [10827x1 double]
C: [10827x1 double]
G: [10827x1 double]
T: [10827x1 double]
Probability =
prob_A: [742x1 double]
prob_C: [742x1 double]
prob_G: [742x1 double]
prob_T: [742x1 double]
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
Bioinformatics Toolbox functions genbankread, traceplot
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