Summary statistics after dada2 questions

Hi!

I am doing tests with QIIME2 for my data (amplicon sequencing form PGM ion torrent in 18S, which we knows that also amplify 16S, so we have different lengths in our amplicon sequences. The different size comes from both genes in the same reaction and that 18S amplicon has variable size depending on the organism; my samples are Mock communities (18, and 3 real samples from marine water)).

I used the forum other times for questions about Dada or deblur because they are not for the moment completely good for my data.

With Deblur my data are not bad at all but the trimming limits so much my analyses, because if I not use very short fragment I loss many sequences about the trimming.

Using dada I cannot know exactly the result because it has not statistics of the command (like deblur). I saw that with verbose I can see in the screen more or less that statistic but only appeared for me in 6 samples (21 in total) and I do not know why. When I convert to vizualizer the table from dada, the file say that I have 21 samples (which is correct) so I do not know why the statistics only appear for 6 samples. Any idea??

Any other option for doing the feature table without trimming??

Thank you very much!
MMC

Hi @MMC_northS - I don’t entirely follow your whole post here, but for this section, does this answer your question?

Please let us know if that answers your question!


These seem to be unrelated to your question above - can you please post as a new, separate question here on the forum? Thanks!

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