HiSeq 2500 run, not hopeful on a quality PE-150 quick run

epistatic · 10-09-2012, 03:04 PM

The data set from the quick run mode on the HS2500 posted isn't too hopeful to have the proposed MiSeq run quality with a shorter run. Is it still spec'd to run PE-150 at a decent % >Q30?

https://basespace.illumina.com/run/1...enome-in-a-Day

>= Q30 90.2% 123.7G
R1 92.9% 63.7G
R2 87.5% 60.0G

GenoMax · 10-10-2012, 04:56 AM

There is probably an inherent assumption that you are willing to sacrifice quality to some extent to get the rapid turnaround.

MiSeq (in specific instances, e.g. 16S multiplexed libraries) is showing similar problems with declining quality in later cycles for 2 x 250 cycle runs.

epistatic · 10-10-2012, 07:47 AM

I am glad I was skeptical when I was told our HiSeq 2500 upgrade would allow >= 80% Q30 on PE-150 runs in the fast run mode and to expect >= 95% Q30 for PE-100. I was hoping to run TSCAP 250 bp capture panels on the HS2500 with PE-150.

We are still very anxious to get the upgrade for quick run times and the ability to run 2 lane flow cells.

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10-09-2012, 03:04 PM	#1
epistatic Senior Member Location: Dronning Maud Land Join Date: Mar 2009 Posts: 129	HiSeq 2500 run, not hopeful on a quality PE-150 quick run The data set from the quick run mode on the HS2500 posted isn't too hopeful to have the proposed MiSeq run quality with a shorter run. Is it still spec'd to run PE-150 at a decent % >Q30? https://basespace.illumina.com/run/1...enome-in-a-Day >= Q30 90.2% 123.7G R1 92.9% 63.7G R2 87.5% 60.0G Last edited by epistatic; 10-09-2012 at 03:24 PM.

10-10-2012, 04:56 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,089	There is probably an inherent assumption that you are willing to sacrifice quality to some extent to get the rapid turnaround. MiSeq (in specific instances, e.g. 16S multiplexed libraries) is showing similar problems with declining quality in later cycles for 2 x 250 cycle runs.

10-10-2012, 07:47 AM	#3
epistatic Senior Member Location: Dronning Maud Land Join Date: Mar 2009 Posts: 129	I am glad I was skeptical when I was told our HiSeq 2500 upgrade would allow >= 80% Q30 on PE-150 runs in the fast run mode and to expect >= 95% Q30 for PE-100. I was hoping to run TSCAP 250 bp capture panels on the HS2500 with PE-150. We are still very anxious to get the upgrade for quick run times and the ability to run 2 lane flow cells.