More Joined than Raw Reads


I used this command to join reads:

qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demuxRound2_050317.qza --o-table tableRound2_050317_290INF.qza --o-representative-sequences rep-seqsRound2_050317_290INF.qza --p-trim-left-f 10 --p-trim-left-r 0 --p-trunc-len-f 290 --p-trunc-len-r 290 --p-n-threads 0 --p-max-ee Inf

and I have more joined reads than raw reads. Can reads be joined to multiple potential mates if max-ee is set to Inf? When I leave max-ee at the default it runs as expected. I didn’t get any errors from the command and everything downstream seems to have worked.



Hi @akknight216! That sounds pretty strange – I’m not sure what’s causing this to happen. @benjjneb, do you have any ideas?

Hi Anna,
I’m not sure how that could be possible.

Could you clarify how are you determining the number of raw reads? And how are you determining the number of reads after denoise-paired?

I used:

for read in `ls *.fastq`; do echo -n "$read "; awk '((NR-2)%4==0){read=$1;total++;count[read]++}END{for(read in count);print total}' $read; done

to count raw reads. To get the joined reads I just used the feature table it printed out after the dada2 step.

Is it certain that these fastq files are not gzipped? Can you share one example pair of fastq files that is showing this behavior?

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