DADA2 -- denoise

[karitorikin (Melih Kaplan)]

hi, below you can find my demux.qzv showing the read quality before DADA2 denoising, I cannot adjust my truncation values properly. I am replicating one of the studies done before and I know the OTU count that they had, yet mine results after all is almost half of it.

How can I adjust my parameters ?
I set this previously.

TRUNC_F=250 TRUNC_R=230 , qiime dada2 denoise-paired \\
--i-demultiplexed-seqs demux.qza \\
--p-trim-left-f 0 \\
--p-trim-left-r 0 \\
--p-trunc-len-f ${TRUNC_F} \\
--p-trunc-len-r ${TRUNC_R} \\
--o-table table.qza \\
--o-representative-sequences rep-seqs.qza \\
--o-denoising-stats denoising-stats.qza \\
--p-n-threads ${CPUS_PER_TASK} --verbose

demux.qzv (312.7 KB)

[colinbrislawn (Colin J Brislawn)]

Hello @karitorikin,

Welcome to the forums!

When working with a new data source, I often run DADA2 several (3-10) times, looking for the best settings to get reads to join.

@karitorikin

I set this previously.

TRUNC_F=250 TRUNC_R=230

Great!

Next, I would try
f240,r230
f240,r220
f230,r220
f230,r210

Have you made the denoising-stats.qzv file and opened it? You can see the percent of reads that merge inside that file!

[karitorikin (Melih Kaplan)]

Yes, I checked the denoising-stats every time after running. Thank you for your help, I guess I’ll do the same !!