I guess I have a weird question, but if I compare my results with the results of other researchers seems like something is wrong.
I have processed 284 soil samples, sequenced by MiSeq 2x275 paired-end (v3-v4 amplicon), whose quality plots looked like this:
After removing the adapters and assuming that the amplicon length is 428 nt, I used DADA2 with many different parameters to choose the best option:
--p-trunc-len-f 240
--p-trunc-len-r 240
--p-trim-left-f 0
--p-trim-left-r 0
Number of ASVs: 39,292
--p-trunc-len-f 246
--p-trunc-len-r 244
--p-trim-left-f 5
--p-trim-left-r 5
Number of ASVs: 35,981
--p-trunc-len-f 240
--p-trunc-len-r 240
--p-trim-left-f 15
--p-trim-left-r 15
Number of ASVs: 38,695
--p-trunc-len-f 230
--p-trunc-len-r 220
--p-trim-left-f 15
--p-trim-left-r 15
Number of ASVs: 54,497
--p-trunc-len-f 230
--p-trunc-len-r 220
--p-trim-left-f 0
--p-trim-left-r 0
Number of ASVs: 55,242
--p-trunc-len-f 246
--p-trunc-len-r 244
--p-trim-left-f 0
--p-trim-left-r 0
Number of ASVs: 55,901
The number of ASVs increased as I truncated more and more the reads, which is the goal I want to achieve. Here, the denoising statistics from the last denoising parameters:
NGS100-21-RUN-1_denoising-stats.qzv (1.2 MB)
However, I have observed that other researchers, even with very similar data, obtain significantly fewer ASVs.... such as 1,000-2,000.
I have been able to assign taxonomy to these ASVs, but still confused.
Is this normal?
How can I check that I have not made any mistakes?