Recommendations for Haloplex on MiSeq

[ArjenB]

Dear users,

We are planning to run Haloplex custom library samples on a MiSeq.
After reading some older posts of 2013, I understand that people sometimes struggled with clustering and low percentages passing the filters, when using pools of 8 or 10pM. Is there any improvement since?
Haloplex pools still can contain some adapter leftovers, what about spiking with PhiX?

Can you give recommendations about the pM of Haloplex pool to load for optimal results, and the percentage of PhiX to use?

Thanks in advance,

Arjen

[dee_em]

Hi Arjen,

We recently did a run of Haloplex on the MiSeq. The details are as follows:

Cluster Density: 1423K/mm2
Clusters passing Filter: 58.4%
%Q30: 83.3
Output: 4.1Gb

I think this was using a 10pM library. In our experience of running Fluidigm panels, the cluster density being so high will significantly reduce the clusters passing filter. I would like to see how an 8pM Haloplex library compares to our 10pM run.

From memory there were about 15 samples on the run, and each one had a minimum of about 50MB of data, some were up to 200MB. It was an experiment by a researcher in our lab, so I don't know too many details.

Hope this helps!