Thanks, I will due that and will post the results. Sorry for my ignorance, but how can you tell in the demux file that only 1/10 of the sequences were merged?
Sounds good!
This info is actually in the stats document you posted, not in the demux itself, since that summary comes prior to denoising.
Ok - but if i´m reading it right it seens that most of the sequences were merged. For example for VitC sample the input was 79027 out of 105833 were merged…
Francisco
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Hi @FranciscoC,
You’re totally right! I just realized I had opened the wrong file once I downloaded your stats file into my temp folder. My apologies! 
Looking at the right file now (and deleted my temp folder too), looks like everything actually went very well and you’ve got loads of successfully merged reads! Sorry for the confusion on this one. I’d say you’re good to move on to your next steps.
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Hi @Mehrbod_Estaki,
No apologies needed. Actually, this help me a lot to understand all the steps and quality checks. Many, many thanks for all the help!!
Francisco
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