Does splitting run reduce read number?

[AKroxy]

If a 454 run is split into 4 separate runs (4 samples), will the total number of reads be smaller than if one full run was done?
Thanks!

[kmcarr]

If a 454 run is split into 4 separate runs (4 samples), will the total number of reads be smaller than if one full run was done?
Thanks!

Are you asking about dividing the picotiter plate into regions using the supplied gaskets? If so then the answer is yes, you do lose some of the total read capacity of the PTP. Portions of the plate are covered by the divider strip of the gasket, the more divider strips on the gasket the more of the plate is covered and unusable for sequencing. By default the plate is divided into two regions. Gaskets are also provided to divide the plate into 4, 8 or 16 regions. Here is what the Roche documentation says are the expected number of reads per region and for the the whole plate for each gasket:

Regions    Reads/           Reads/
        Region (10^3)     Run(10^3)
 2        450-650         900-1300
 4        160-250         640-1000
 8         80-120         640- 960
16         25- 40         400- 640

The alternative is to use multiplexed ID tags (bar codes) and then mix your samples together. Discuss with your sequencing facility the costs and benefits of each method.

[AKroxy]

Thanks tons, kmcarr, that's exactly what I needed to know!
Going from 2 to 4 sections actually seems like a substantial reduction in data (>23%)