Cross-post: Is trimming beneficial for RNA-Seq??

The following commentary is a cross-post from MacManes Lab (Using genomics to understand adaptation in non-model organisms). In our own work, we try to avoid read- trimming as much as possible, because the trimming process introduces an additional arbitrary parameter in the assembly process, which is not needed. The de Bruijn graph-based assembly process is supposed to take care of the low-quality ends of reads in the ‘tip removal’ step. Someone inclined to do read trimming should play with tip-removal parameters instead of trying to find optimal quality for trimming.

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