losing large amount of reads when using Qiime2 vsearch joinpairs command
Hi there! I am running various sediment samples (Illumina for amplicon 16S – V4V5 sequencing) through the Qiime2 pipeline, however when I use vsearch joinpairs to join my paired end reads I lose a bunch of reads. For reference, here is a breakdown of my workflow for one sample:
Before trimming reads = 79 489 reads
after trimming = 75 542 reads
after joining = 28 005 reads
after filtering = 28 004 reads
Could anyone give some explanations as to why this may be happening? I figured there may be a few reasons but hopefully someone can help
Here is the command I used
qiime vsearch join-pairs –i-demultiplexed-seqs csm-vs-birds/PE-trimmed-reads.qza –o-joined-sequences csm-vs-birds/PE-trimmed-joined-reads.qza
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