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Old 10-12-2014, 10:48 AM   #1
stasi
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Location: Israel

Join Date: Feb 2013
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Unhappy wrong run parameters. How can I change it after 1 cycle?

Hi.
Please help me. I started a run (Hi seq 2500, Rapid mode) and by mistake set following parameters:
Read 1: 100
Index1: 9
Index2:100
I meant to run Read 1: 100, single index of 8 bp and read 2: 100.
I noticed that where is a mistake and stopped the run after 1st cycle.
I tried to resume the run and was surprised that hiseq doesn't allow me to change the run parameters
Is anyone had the same issue in the past and can help me? PLEASE
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Old 10-12-2014, 08:54 PM   #2
kcchan
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You can do a primer rehyb on your flow cell and restart the run. Call Illumina tech support and they can help you with that.
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Old 10-12-2014, 10:19 PM   #3
nucacidhunter
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Other options are to let the run to continue and add the 9th base from the adapter to all indices or during demultiplexing mask the 9th base from your index reads.
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Old 10-13-2014, 12:31 AM   #4
kcchan
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Quote:
Originally Posted by nucacidhunter View Post
Other options are to let the run to continue and add the 9th base from the adapter to all indices or during demultiplexing mask the 9th base from your index reads.
Unfortunately that won't help him with the 100bp index 2 read. After 8 bases you'll end up with a bunch of adapter sequence followed by read 1 all over again.
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Old 10-13-2014, 01:32 AM   #5
nucacidhunter
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Quote:
Unfortunately that won't help him with the 100bp index 2 read. After 8 bases you'll end up with a bunch of adapter sequence followed by read 1 all over again.
You are right. I thought it was read 2 not index 2.
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