All of my reads do not merge after using native cutadapt. The vast majority failed to merge due to staggered read pairs, according to the log from
qiime vsearch join-pairs.
First, I used native cutadapt to remove forward and reverse primers from my paired-end Illumina sequences (V4 region) using the command below. My primers are: 515fXT (GTGBCAGCMGCCGCGGTAA) and 806rXT (GGACTACHVGGGTWTCTAAT). As you can see in the log below, primers were detected in over 90% and over 90% of the read pairs were written. This was the case for pretty much all of the fastq pairs.
Generic cutadapt command:
cutadapt --cores=0 -g GTGBCAGCMGCCGCGGTAA -G GGACTACHVGGGTWTCTAAT --discard-untrimmed -o R1.cutadapt.fastq.gz -p R2.cutadapt.fastq.gz R1.fastq.gz R2.fastq.gz >> primer_trim.log
Then I tried to merge using vsearch join-pairs:
qiime vsearch join-pairs --i-demultiplexed-seqs demux.cutadaptgG.qza --o-joined-sequences demux.cutadaptgG.merged2.qza --verbose
Here are the quality graphs:
Any ideas why nearly 100% do not merge?