Splice aware vs splice unaware aligners?

Splice aware vs splice unaware aligners?

2

Hello, I would like a clear and simple answer on the difference of splice aware / splice unaware aligners. There is a discussion that @dfernan generated but for me the definition is not very clear. Can you help me please. 😀


aware


unaware


aligners


splice

• 48 views

splice aware aligners take into account to ‘split’ the alignment only when it is compliant to the correct use of splice sites (donor & acceptor site , most typical setting: GT-AG )

splice un-aware aligners can ‘split’ their alignment as they see best (== maximizes their alignment score) and thus not necessarily making use of correct donor-acceptor site usage.

Splice aware aligners like tophat, STAR provide bam out put with spliced junction information (specific locations where introns are removed) whereas non splice aware aligners like bowtie2 do not do this.


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