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Old 11-07-2011, 12:41 PM   #1
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Default Changing HiSeq Parameters Mid Run

I accidentally set my index read as 10x as many cycles as I would like to sequence, and I am through most of my 1st read. Does anyone know how to change the parameters for the index read while a run is in progress?
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Old 11-09-2011, 07:03 AM   #2
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You have to ring Illumina tech support I'm afraid, they can remotely access the HiSeq and change the run parameters.

I've forgotten to put an index on one of my runs before and they managed to sort it this way.
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Old 03-11-2012, 08:12 AM   #3
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I understand it is too late for you now, but in principle changing paramaters mid-run is easy: you kill HCS, change parameters in the config files, restart. Since you discovered problem during cycle 1 and the barcodes are read at the end changing these parameters should create no issues. It is more tricky if you want to change parameters that are important early on later in the run. If you are still interested, let me know to post details about config files to be changed
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Old 12-11-2018, 02:29 AM   #4
Location: Brno, Czech Rep.

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Hello, If you can read this in time - can this be done with miseq instrument ? I need to make him sequence dual indexing instead of single indexing, so if you know which files to modify.

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Old 12-11-2018, 08:07 AM   #5
Location: Livermore, CA

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Yes, MiSeq should be in the same boat. If you kill the run, it shouldn't write out to the RFID's so the cartridge and flow cell would still be useable. However, you'll have to change the recipe fragments so that when it goes to perform cluster generation it only does something mild like a PR2 delivery. MiSeq won't let you resume a run like HiSeq will.
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