Question about LSK114 primer sequences

[cjops]

When using the edlib backend, I noticed that the primer sequences included in LSK114_primers.fas are very similar to the default cDNA_SSP_VNP.fas. In fact, as far as I can tell from the protocols for kit PCS109 and kit LSK114, these sequences haven't actually changed.

From Chemistry Technical Document July 8th, 2021:

From Direct cDNA Sequencing V14 with SQK-LSK114 protocol:

In our data, generated with the new kit LSK114, the more complete version of the primers included in cDNA_SSP_VNP.fas leads to more usable reads. Was there any rationale behind using the shorter form of the primers for the new kit?

[nrhorner]

Hi @cjops

These primer sequences were chosen from empirical observation when testing primer sequences on a limited number of datasets. What recovery rate do you get with using both sets of primers?

[cjops]

I see, thanks! We've only done one run on a single flow cell so far, but this is with cDNA_SSP_VNP.fas (pychopper -m edlib, defaulting to PCS109):

And this is with LSK114_primers.fas (pychopper -m edlib -k LSK114):

We're generating more data and I'll see which primer sequences perform best for that as well.

[nrhorner]

@cjops Thanks for sharing those, it's useful.

[nrhorner]

Closing due to lack of response