As part of the Primary Analysis Illumina sequencing machines measure the intensity of the channels used for encoding the different bases and identify the most likely base at a given position of a sequencing read (tag). The Real Time Analysis (RTA) software writes the base and the confidence in the call as a quality score to base call (.bcl) files. As the name implies this is done in real time, i.e. for every cycle of the sequencing run a call for every location identified on the flow cell (tiles and lanes) is added. Bcl files are stored in binary format and represent the raw data output of a sequencing run. The format is described here. Software such as Casava/BclToFastq, Eland or the iSAAC aligner can make use of these files.
The *.bcl files are stored in the BaseCalls directory:
<run directory>/Data/Intensities/BaseCalls/L<lane>/C<cycle>.1
They are named in the format:
s_<lane>_<tile>.bcl
If you want to overcome errors during downstream processing from missing calls, software such as iSAAC and configureBclToFastq have an “–ignore-missing-bcl” command line option. This will interpret missing *.bcl files as no call (N) at that position.
Sources: Illumina, SeqAnswers