I've heard that trimming is not as efficient as alignment in the pipeline and then building up or down from there.
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Could you elaborate? What do you mean by 'efficient'?Comment
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i think the small rna pipeline will use the adapter sequence to more efficiently trim reads. It's better to run them as 35bp than to trim them and try and map.Comment
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cutadapt and most trimmers I know do use the adapter sequence to trim the reads (they align the adapter sequence to the end of the read). The alternative is to unconditionally remove the last x bases (or colors) of each read. I do not consider that to be adapter removal, it is way too inaccurate.Comment
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