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Bcl Files

The *.bcl files can be found in the BaseCalls directory:

<run directory>/Data/Intensities/BaseCalls/L<lane>/C<cycle>.1

They are named as follows:


The *.bcl files are binary base call files with the format described below.



Data type

Bytes 0–3

Number N of cluster

Unsigned 32bits little endian integer

Bytes 4–(N+3)

Where N is the cluster index

Bits 0-1 are the bases, respectively [A, C, G, T] for [0, 1, 2, 3]:
bits 2-7 are shifted by two bits and contain the quality score.

All bits ‘0’ in a byte is reserved for no-call.

Unsigned 8bits integer



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