Paul Shinn wrote:
> We received our Collection 1.1 upgrades 2 weeks ago and I'm testing
> out the POP5 that has been so heralded by PE for it's improved run time
> and longer average read length. Well, I do like 1.1 better than 1.0 and
> the shorter run time certainly has possibilities. However, the quality
> of the data I'm getting out of it just doesn't seem up to par with my
> other 3700 using 1.0 and POP6.
> The signal intensity is not as even across the capillary but that
> isn't my main beef. The problem I'm having is that I'm missing bases in
> my sequences.
> [...]
Paul,
Like you, I've just started using POP5 and v 1.1. I looked over about 50
chromats last night and this morning but didn't see the peak drop-outs that
you are seeing. That doesn't mean there aren't any, but I haven't found any
yet.
What results am I getting from POP5? The main peak of number of phred20
bases increases by about 50 bases--but I get more failures and marginal
reads. Hence the total number of phred20 bases/run actually decreases. But I
hope to tweak some parameters and see more benefits from POP5. It looks like
many of my capillary plumes have shifted and need to be tuned up a little. I
might need to run a new spatial.
Do you see these drop-outs using PE's basecaller/chromat viewer or are
you only looking at results from a third-party basecaller (eg, phred)?
Phillip San Miguel
Purdue Genomics Core Facility
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