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  • #16
    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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    • #17
      Could you elaborate? What do you mean by 'efficient'?

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      • #18
        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.

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        • #19
          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.

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