losing large amount of reads when using Qiime2 vsearch joinpairs command

losing large amount of reads when using Qiime2 vsearch joinpairs command

0

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


16S


Qiime2


amplicon


joining

• 99 views

Read more here: Source link