Reads Loss during DADA2 run

[mentorwan]

We ran a full-length Pacbio DADA2 analysis. Here is a question we encountered during the process:
There is some minor read loss during the DADA2 process. For example, in one sample, stats.tsv shows 24,049 non-chimera reads, but the DADA2-generated biom file or qzv file or taxonomy table shows only 24,025 reads—a loss of 24 reads.

I previously thought the number of reads would match the number of non-chimera reads after QC. Although this read loss is minimal, I checked other samples: some show no loss while others have very few lost reads.

Maybe it’s not a significant issue. Could you clarify our understanding or provide any related information we might be missing? Thanks.

[benjjneb]

For example, in one sample, stats.tsv shows 24,049 non-chimera reads, but the DADA2-generated biom file or qzv file or taxonomy table shows only 24,025 reads

Can you clarify what workflow you are using and how these different numbers are being generated?

[mentorwan]

The workflow we use is HiFi Full length 16S workflow: https://github.com/PacificBiosciences/HiFi-16S-workflow

The number is generated by output from this pipeline.
Here is table in stats.tsv related to this sample:

sample-id	input	filtered	denoised	non-chimeric	percentage of input non-chimeric
SC830317	39431	24600	24132	24049	60.99

But in DADA2_table.qzv file, we can see that for this sample, only 24025 reads assigned. There are 24 reads differences.