Can anyone advise me about this issue? after running the command below
qiime dada2 denoise-paired
--p-trim-left-f bp of primer F
--p-trim-left-r bp of primer R
--p-trunc-len-f length of best quality
--p-trunc-len-r length of best quality
--p-n-reads-learn How many times it tries
--p-n-threads unlimited (0)
I got only few merged sequences. would be possible to adjust the command to get more sequences? Ex the input was 29004 but only 8 sequences were merged.
See the attached file.
Could you briefly describe your experimental design？Which amplicon you sequenced? Which sequencer and how long is the amplicon? Also upload your demux.qza so we can find what is the issue.
Can you post your exact values for your trim and truncation parameters? These often cause the problem as there aren’t enough quality bases left to merge on.
Can you share your read quality as well? It helps determine optimal parameters. I got mine in R following the dada2 tutorial https://benjjneb.github.io/dada2/tutorial.html
In fact I tried to use short length of forward and reverse sequence (180, 210). When I increased that (240, 230) worked well.