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Cross-posted on bioinfo SE: https://bioinformatics.stackexchange.com/questions/21118/how-to-calculate-the-variant-allelic-fraction-vaf
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how is this post different from your previous post? <https://www.biostars.org/p/9565445/#9565445>
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You can `cat` the respective R1/R2 files in same order e.g. `cat Run1_R1.fq.gz Run2_R1.fq.gz > R1.fq.gz`.
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Exactly. I agree that this is due to the NovaSeq which is not very compatible with qimme2 DADA2 pipeline. I finally surrendered to other ap…
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Thanks for your quick reply! How would you merge them?
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My guess is that some samples were resequenced. I'd recommend just merging the respective R1 and R2s and treat them as one sample.
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