There are four different methods for removing adapter sequences in the
Alignments vignette of Biostrings (which was the basis for one of
Patrick's courses at BioC 2008):
http://bioconductor.org/packages/2.3/bioc/vignettes/Biostrings/inst/doc/Alignments.pdf
But the srdistance() method appears to be faster.
Best,
Jim
Cei Abreu-Goodger wrote:
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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James W. MacDonald, M.S.
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