25 bp/frag run vs 50 bp/frag run regarding N2S ratio and cost efficiency

smallcreek · 12-01-2009, 10:32 AM

Hi,
I am a newbie for Solid NGS. Our customers are mostly from academic professors who place orders to run a few of samples (2 samples most recently).
I realize that 25 bp/frag run can cut cost significantly because of two reasons:
1. the price per sample can be reduced 30%
2. when a customer needs to run only 2 samples, the whole flowcell run cost from the strip and buffer reduced 65%, assume the left 7 packages of the strip buffer will not expire before they are used for other customers.

I have two technical questions about 25 bp vs 50 bp.

1. It seems N2S ratio goes up after 25 bp cycles. Is that true that we get more matching beads/aligned reads if we do 25 bp run rather than 50 bp run?
2. It seems the total tag coverages between 25 bp and 50 bp are not too much different on a segmetn of a quad slide. Does 50 bp run have many other advantages over 25 bp run?

Thanks in advance,

smallcreek

smallcreek · 12-02-2009, 05:47 AM

I talked with our FAS and he mentioned the GB throughput is difference between the 25 bp and 50 bp run. But he also acknowledged the N2S ratio for 50 bp run can go much higher at the end of 10 cycles run.
I am still not clear about the other major difference between these two.

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12-01-2009, 10:32 AM	#1
smallcreek Junior Member Location: Florida Join Date: Nov 2009 Posts: 4	25 bp/frag run vs 50 bp/frag run regarding N2S ratio and cost efficiency Hi, I am a newbie for Solid NGS. Our customers are mostly from academic professors who place orders to run a few of samples (2 samples most recently). I realize that 25 bp/frag run can cut cost significantly because of two reasons: 1. the price per sample can be reduced 30% 2. when a customer needs to run only 2 samples, the whole flowcell run cost from the strip and buffer reduced 65%, assume the left 7 packages of the strip buffer will not expire before they are used for other customers. I have two technical questions about 25 bp vs 50 bp. 1. It seems N2S ratio goes up after 25 bp cycles. Is that true that we get more matching beads/aligned reads if we do 25 bp run rather than 50 bp run? 2. It seems the total tag coverages between 25 bp and 50 bp are not too much different on a segmetn of a quad slide. Does 50 bp run have many other advantages over 25 bp run? Thanks in advance, smallcreek

12-02-2009, 05:47 AM	#2
smallcreek Junior Member Location: Florida Join Date: Nov 2009 Posts: 4	I talked with our FAS and he mentioned the GB throughput is difference between the 25 bp and 50 bp run. But he also acknowledged the N2S ratio for 50 bp run can go much higher at the end of 10 cycles run. I am still not clear about the other major difference between these two.