Opened 9 years ago

Closed 9 years ago

#730 closed enhancement (fixed)

Set target molarity in "Create pooled libraries" wizard

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v3.1
Component: net.sf.basedb.reggie Keywords:


In the current wizard, the target molarity is fixed at 2nM. This was selected since the clustering protocols for the sequencers required this concentration.

However, the NextSeq have variants were the pool molarity can be different (for example 1nM). This can be an advantage if the molarity of libraries are low and it is difficult to reach 2nM for the pool.

The "Create pooled library" should have an option to specify if the target molarity should be 1 or 2 nM. Subsequent calculations for the mixing protocol should take this into account.

Since this also changes the clustering protocol we need to verify pool molarity in the "Create flow cells" wizard. When creating HiSeq flow cells, we should only allow pools close to 2nM. When creating NextSeq flow cells we can allow any molarity, but when close to 1nM we need to use 20µl instead of 10µl.

This must also be visible in the clustering protocol so that the correct amount is taken and the proper mixing tables are used from the protocols.

Change History (4)

comment:1 by Nicklas Nordborg, 9 years ago

Status: newassigned

comment:2 by Nicklas Nordborg, 9 years ago

(In [3107]) References #730: Set target molarity in "Create pooled libraries" wizard

Added selection list in "Create pooled libraries" wizards (both the plate-based and manual) that allows selecting target molarity to 1.0 or 2.0 nM.

This information is already visible in the lab protocols for pooling so no change was needed there.

comment:3 by Nicklas Nordborg, 9 years ago

(In [3108]) References #730: Set target molarity in "Create pooled libraries" wizard

Display pool molarity in "Create flow cells" wizard and make some checks that selected pools have expected molarity (eg. HiSeq requires 2 nM pools).

New selection list for selecting 10/20 µl to take from the pool. Default selected is 20 if the pool molarity is close to 1 nM and 10 otherwise).

Display pool molarity in the cluster and sequencing lab protocol if it is not 2 nM. Amount to take from the pool can't reliably be displayed since it depends on if one or two flow cells are selected.

comment:4 by Nicklas Nordborg, 9 years ago

Resolution: fixed
Status: assignedclosed
Note: See TracTickets for help on using tickets.