eba -- Estimates Base Accuracy in an SCF file
eba [scf_file]
Eba will calculate numerical estimates of base accuracy for each
base in an SCF file. The figures calculated should not be considered as
reliable. The long term aim is that the program will be redundant as
each sequencing machine vendor should create their trace files with the
base accuracy figures already calculated.
The method employed by eba to estimate the base accuracies performs the following calculation for each base. Calculate the area under the peaks for each base type. Divide the area under the called base by the largest area under the other three bases. Normalise this figure to a value between 1 and 99. 99 represents the highest accuracy; 1 the lowest.
With no filename as an argument eba reads from standard input and writes to standard output. This enables eba to be used as a filter, or to estimate base accuracies for unwritable files. If a file is specified on the command line then the accuracy figures will be written to this file.
To write base accuracy figures to an SCF file named e04f10.s1SCF.
eba e04f10.s1SCF
To write base accuracy figures to an SCF file named e04f10.s1SCF
in another users directory, and to store the updated file in the
current directory:
eba < ~user/e04f10.s1SCF > e04f10.s1SCF
See section scf(4).