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Old 02-18-2015, 04:54 PM   #1
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Location: South Australia

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Default HiSeq2500 - how to sequence pair after single end run

Our machine was prepped for a Paired End run, but we forgot to enter the read length for the paired read, so the machine ran it through as single end.

The job has completed, and the flow cell is sitting there.... it seems that all we would need to do is convince the Illumina software to turn the molecules over and start the second run.

Illumina tech support say this is impossible.

Does anyone know how to save this run?

I renamed/move all of the files produced during the run (netcopy files, Processing & Data directories), modified the runParameters.xml and restarted the program, hoping to resume a sequencing run, but it didn't work.

Edit: Idea

We have thought of an idea, which is to do a second run, with 0 bases (or 1) for the first read, then continue on with the pair. We can then match reads from the 1st run with the 2nd via tile ID.

Does anyone have any comments on whether this would work?

Last edited by dlawrence; 02-18-2015 at 05:06 PM.
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Old 02-19-2015, 01:26 PM   #2
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I don't think you'll be able to do another run with 0 bases, because the instrument will try to carry out clustering again, which would probably be bad for your already clustered flowcell.

I suspect that you might have to start again.


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Old 02-19-2015, 03:29 PM   #3
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I doubt this is possible, IME Illumina's tech support will tell you off-label ways to do things (with disclaimers) if they know how it's possible.

You will not be able to match up the new read2's because the XY positions of the clusters will be different.

Also, moving this to Illumina forum.
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Old 02-19-2015, 08:41 PM   #4
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The most straightforward option is to rehybridize the flow cell and start a new paired-end run. You lose the existing read one data, but salvage the PE flow cell/clustering. It might be technically feasible to modify the existing run data to convert it to a paired end run and restart it but, without guidance from Illumina, it's virtually impossible to determine which of the many files require editing to make this work.
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hiseq 2500, hiseq paired end

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