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Old 11-02-2010, 12:14 PM   #8
Location: denver, co

Join Date: Apr 2010
Posts: 72

just to clarify, you are counting uniquely mapped reads, correct?
clearly, shorter reads will be more likely to map ambiguously--that is they can map to multiple places in the genome.
[fwiw, i work with illumina and *always* check them in FastQC then trim with fastx-toolkit]
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