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.

So depending on the purpose in mind, picking 5 million reads from the
middle of the file might be fine (and much easier computationally).

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