This strikes me as something best done with a wrapper / separate program. We want to avoid including features in Bowtie that are this situation-specific.
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I envision trimming 3' adaptor on an as needed basis - if the read aligns to the fasta database without trimming, then, then emit that alignment, otherwise trim as little as 3' adaptor as possible to make the alignment
such ability would be of benefit to how we're using bowtie
novoalign appears to have such a feature - however it is not "as needed"
This strikes me as something best done with a wrapper / separate program. We want to avoid including features in Bowtie that are this situation-specific.
Ben - I think I disagree.
I envision trimming 3' adaptor on an as needed basis - if the read aligns to the fasta database without trimming, then, then emit that alignment, otherwise trim as little as 3' adaptor as possible to make the alignment
such ability would be of benefit to how we're using bowtie
novoalign appears to have such a feature - however it is not "as needed"
http://www.novocraft.com/wiki/tiki-index.php?page=3+Prime+Adapter+Stripping&structure=Novocraft+Technologies
in any case, fastx-toolkit can be used to pre-trim adaptor: http://hannonlab.cshl.edu/fastx_toolkit/
Cheers
Malcolm Cook