Determine how wet lab models inputs for amplicon pool library plates and decide on interface changes to address

[AmandaBirmingham]

Raised in amplicon walkthrough 07/30/2018

Details from email thread:

From MacKenzie:

I've been thinking about how to change the wording on the pooling parameters for Labman. Usually we think of the pooling volumes/cutoffs I'm not sure in terms of, "If the concentration is greater than X, we pool X. If it is lower than X, we keep it how it is." Currently Labman's settings are basically "If the concentration is lower than 16 ng/mL, then we will pool 2uL of the sample." I'm trying to figure out a way to word this in a more intuitive way for the parameters on Labman.

From Jon: What the wet lab has been doing for pooling 16S has been, per my understanding from previous discussions:

• measure library concentration (ng/µL)
• divide desired pooled quantity (240 ng per sample) by the concentration (µL) to get estimated pooling volume
• for samples above a threshold volume (typically 15 µL), pool them at a default, lower volume.

Note that the 'above this value' number is actually a volume, and not a concentration.

in Labman, the same exact operation is being performed, except that it's being thresholded based on the concentration instead of the pooled volume. This enables the pooling to be calculated independently of total volume, which is important to allowing the same basic pooling algorithm to be used for different library prep types. It's also, in my mind, more intuitive, as samples below a threshold are affected, and the point is to adjust the pooling volume of samples that have low concentrations libraries.

So on Labman:

• measure library concentration (ng/µL)
• for samples below a threshold concentration (16 ng/µL, which == 240 ng / 15 µL), pool them at a default, lower volume.

[charles-cowart]

Tentatively moving to Nice To Haves.