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Old 04-02-2013, 02:47 PM   #2
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Location: San Diego

Join Date: May 2008
Posts: 912

Bioinformatically, there's nothing you can do, other than help the people to know what went wrong.

For starters, spot-check some random high quality reads, BLAST them against nr, see if you can determine what they are.

Try aligning to the whole genome to see how much of the library was genomic.

See if there are certain highly repetitive reads (like Illumina adapters) taking up a lot of reads.

And of course see if the run overall was of good enough quality for you to believe that your reads are accurate.
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