Hi Martin,
It would be nice if the ShortRead QA report could somehow filter out the
adapter contamination before generating the rest of its plots, since those
plots are pretty meaningless if there are adapters present.
Not sure how to handle this filtering in general. That is, what if someone
then wants to see plots with only the "high quality" reads after the quality
plots. It gets complicated. ShortRead has a nice filtering mechanism, but
this is more complicated, since some QA plots come from one filter, while
others come from a different stage.
However, under the assumption that no one would ever want to align an
adapter, i.e., those reads will not be carried forward, the adapter removal
could just be treated specially hard-coded. And then just expect more
customized solutions to leverage the internal ShortRead functions for
generating each slot in the QA object, building it up incrementally, on
different subsets. Of course, to make sense, that would require a different
report template, too.
Michael
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