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Old 03-13-2015, 04:09 AM   #17
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Location: uk

Join Date: Mar 2009
Posts: 667

The problem that you describe in the first few bases is often seen with RNA-Seq data,
and is thought to be due to the random priming being not so random in practice.

This has previously been disussed in various threads, one of which is here:

The trimmomatic adapter trimming only trims adapter sequences from the 3' ends of the reads.
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