support for adapters known to be ligated to the 3' end

[marcelm]

From marcel.m...@tu-dortmund.de on December 01, 2010 18:33:19

It should be possible to specify that an adapter should only be found in the 5' end or the 5' end of a sequence.

Original issue: http://code.google.com/p/cutadapt/issues/detail?id=1

[marcelm]

From marcel.m...@tu-dortmund.de on December 08, 2010 03:36:02

That should of course read "in the 5' end or the 3' end of a sequence".

This issue was added in response to a user request which was based on a misunderstanding of the small RNA protocol that was used. The actual request should read:
It should be possible to specify that an adapter should only be found in the 3' end of a sequence. In other words, the knowledge that the adapter is always ligated to the 3' end should be used.

This has now been implemented: The -a parameter's default behavior is now to assume that the adapter was ligated to the 3' end. This is probably what most people want.

If you want the old behavior, use the -b option (see documentation for details).

Summary: support for adapters known to be ligated to the 3' end
Status: Fixed