[Bioc-sig-seq] adapter removal

[James W. MacDonald]

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.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-5646
734-936-8662