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Supplement for Methods in Molecular Biology 2018
This pipeline and tutorials are incredibly useful! I'm playing now with the diamond to seed section, and I'm wondering if the strategy is to only map the reverse reads. If I'm not mistaken, DIAMOND can't handle paired files. One strategy is to merge the reads, but am I correct in my interpretation that your scripts only align the reverse R2 reads? Does that provide the same outcome as first merging the reads? Or perhaps this is reconciled downstream in the code in a way that I didn't recognize. Any further clarification would be greatly appreciated.
THANKS!
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