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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I do not think there is an option to do this. -
So when the sequencer is running where does the data get stored while the machine is running? Is it on the instrument itself or does the data flow to a data store somewhere.Comment
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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.Comment
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Thanks for the Info Jessica, just what I was looking for.Comment
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