I was curious if Illumina sequencers allow you to read the raw FastQ files they are producing while they are running. I'm trying to see if you really have to wait for the sequencer to finished before you start the alignment.
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Depending on the instrument and your settings, you may see either. The HiSeqs have temp folders on the computer's D and E drives that hold the cluster intensities and .bcl files; MiSeqs are analogous-- there's an output folder location specified during run setup, in addition to the analysis folder. You can specify those temp locations to be a network location, if you want.
I don't happen to recall if basespace also gets copies of the .bcl files mid-run.
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