to the best of my knowledge reads at the start of SOLiD data set also have
a higher error rate ..
I think it might be also due to edge effect.


On 9 November 2011 21:49, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> On Wed, Nov 9, 2011 at 12:03 PM, Bob Harris <rshar...@bx.psu.edu> wrote:
> > David, in my experience with Illumina sequencing, it looks like the
> reads at
> > the start of a file have a much higher sequencing error rate.
> > Bob H
>
> Yes, reads at the start and the end of the file come from the edge of
> the Illumina slide, and tend to be of poorer quality that the reads from
> the middle.
>
>
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