Increasing number of nonchimeric reads compared to the number of input reads

[Abdelrahim-maker]

Hi everyone

I was using dada2 in R on my arbuscular mycorrhizal fungi reads and I noticed that after truncating them, I got an increased number of nonchimeric reads compared to the input I had. for example my input for one of the samples was 666 reads and the nonchim is 47,000. another sample has an input of 8 and nonchim which is 49 reads. How is that possible?

Thanks

[benjjneb]

It's not possible. How are you arriving at this result?

[Abdelrahim-maker]

@benjjneb apologies for the late reply. That is how I was doing it Parameters used:
filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=c(280,275),
maxN=0, maxEE=c(2,2), trimLeft = 10, truncQ=2, rm.phix=FALSE,
compress=FALSE, multithread=n_cores, verbose = TRUE)
overall Median loss (difference between input and nonchimeric) = 15311, percentage= 46.99108
Overall minimum percentage loss = 32.5477
Overall maximum percentage loss = 100

[benjjneb]

Can you provide the output of read tracking through the workflow, as demonstrated in the read tracking section of the dada2 tutorial? https://benjjneb.github.io/dada2/tutorial.html#track-reads-through-the-pipeline

[Abdelrahim-maker]

16s_reads_summary (1) (1) (2).csv
densoised_reads_amf (5) (2).csv

These are the output for AMF and 16S rRNA which I have noticed issues after using these parameters

[benjjneb]

Can you clarify what your issue is? I do not see the examples that you referenced in your first post, nor any sample where the number of nonchimeric reads is more than the input.