[Bioc-sig-seq] adapter removal

Cei Abreu-Goodger cei at ebi.ac.uk
Wed Jan 14 18:19:55 CET 2009


> 
> Yes you're right the context I'm thinking of is that one wants to
> remove reads ('filter') that have adapters, rather than removing the
> adapter sequence ('edit'?). My thinking is that the reads are short
> and numerous anyway, so little information is lost even when 10's of
> thousands of reads are filtered, and the filtered reads are more
> suspect than normal anyway because of the presence of the
> adapter. This might be relatively naive.
> 

Just a brief comment on this. An example of when it could be useful to
edit the reads to remove adapter sequence is for small RNA sequencing
(miRNA, etc). In these cases, the biological entity which you're
sequencing will mostly be of a shorter length than the total read
(~17-26 lets say). In this case it becomes very useful to be able to
remove (or mask out) only the adapter sequence.

Cheers,

Cei



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