Lose many reads after running cut-adapt and join-pairs

[sjcochran (Sam Cochran)]

Thank you so much! It looks like --p-allowmergestagger took care of my issue completely. I am retaining 10x the number reads now. Your advice also helped me find another topic thread which used vsearch join-pairs --verbose to estimate the number of reads that failed to join, specifically because of staggering. Linking it here so others can find:

Most reads failed to merge due to staggered read pairs

Dear q2-ers, 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 re…

I tried this without --p-allowmergestagger and it looks like staggered read pairs were the primary reason my joins failed.

Thanks!
-Sam