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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).

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.