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This means that rather than actual estimated concentrations being stored in the DB, we are storing some actual concentrations (high-conc samples) and some fake concentrations (low-conc samples and blanks), then doing a trivial calculation in the pooling method:
Additionally, Greg requests some ability so selectively choose the number of blanks to pool (e.g in a plate with lots of high-conc blanks, might want to sequence several to see what's going on).
...
I suggest the following:
Consolidate the concentration logic for 16S and shotgun libraries into a single method. They're fundamentally the same: just estimating molarity based on DNA concentration and average fragment size. There's no reason to separate them.
Consolidate the pooling logic for 16S and shotgun libraries. The 16S method is identical to the 'min-vol' method for shotgun, with the exception that blanks are treated specially. No reason not to use the same methodology here and just pass parameters to affect behavior. The parameters should be defined by the js interface.
Expose the blank-selection criteria in the interface, and modify heatmap plots such that included blanks are visually differentiated (changing emojis for those wells?)
The text was updated successfully, but these errors were encountered:
Currently, amplicon quantification and pooling doesn't work correctly.
The way the wet lab does amplicon pooling currently is that it:
But what's happening in the code currently is that the first three elements of this are (sort of) happening in the concentration calculation:
https://github.com/jdereus/labman/blob/7a4df3170e6a511336fdb7294521999b34d3df77/labman/db/process.py#L1825-L1833
This means that rather than actual estimated concentrations being stored in the DB, we are storing some actual concentrations (high-conc samples) and some fake concentrations (low-conc samples and blanks), then doing a trivial calculation in the pooling method:
https://github.com/jdereus/labman/blob/7a4df3170e6a511336fdb7294521999b34d3df77/labman/db/process.py#L1866-L1881
Additionally, Greg requests some ability so selectively choose the number of blanks to pool (e.g in a plate with lots of high-conc blanks, might want to sequence several to see what's going on).
...
I suggest the following:
The text was updated successfully, but these errors were encountered: