Hi all, I am new in QIIME2 and I am working with paired end reads that came direct from Illumina sequencing. So I have three archives that I imported with the command: qiime tools import --type EMPPairedEndSequences --input-path paired-end-sequences --output-path paired-end-sequences.qza And then…

Hi @cintia_martins ! How are you choosing your trim and trunc length parameters? There are lots of good discussions of that here on the forum (incl. 1 , 2 ), as well as in the Atacama tutorial , and in the DADA2 docs . It's common to lose sequences if DADA2 does not have enough nucleotides to successfu…

[image] ChrisKeefe: 2 Hi @ChrisKeefe ! It worked! I changed trunc values for my reverse reads. I don’t know why I was fixing the same values for forward and reverse… I am testing some different values and I am getting good sequence count with --p-trim-left-f 100 --p-trim-left-r 100 --p-trunc…

@cintia_martins , I'm glad that helped! Have you tried setting your trim-left values lower (possibly even to 0), and keeping the new truncate values that are working for you? I'm curious about whether you couldn't squeeze more sequences out of this set, or at least preserve all of that high-quality …

Hi ChrisKeefe! With lower setting I don't get much improve. With --p-trim-left-f 25 --p-trim-left-r 25 --p-trunc-len-f 260 --p-trunc-len-r 180 I got the following: [27] [45] And with --p-trim-left-f 100 --p-trim-left-r 100 --p-trunc-len-f 260 --p-trunc-len-r 180 I got the following: [39] [50…

Thanks again for sharing the details, @cintia_martins ! :slight_smile: I talked with the QIIME2 team, and this is the first time we've seen better sequence counts with the high trim-left arguments you passed. Hopefully, it's all smooth sailing from here, but if you run into issues, you might use Fas…

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Low sequence count after DADA2

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