What Bruce suggested is the current way of getting assignment stats from using featureCounts. But apparently it is not user-friendly. It is on our to-do list to output assignment stats (with no need to turn on -R option) when read summarization is done, but it will take a week or two to implement it. We will make a new release in a day or so, but it is not going to be included in that release.
Best,
Wei
Best,
Wei
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