You might want to make a quick search of the archives.  There was just a
discussion about this topic a week or so ago.

Sean

On Mon, Feb 9, 2009 at 10:39 PM, Bogdan Tanasa <tanasa@gmail.com> wrote:

> Hi all,
>
> would be glad to have your answer to a question (that is probably very
> simple):
>
> we do have a set of small RNA solexa sequences, where the length of the
> read
> is 36.
> we suspect that the adaptors sequences are present in the solexa reads, at
> various
> positions and for various lengths. is there a quick way to mask the
> adaptors
> sequences
> in the reads before doing the alignment process ? thanks very much,
>
> -- bogdan
>
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>
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