I am working with a set of demultiplexed data, so I followed Alternative methods of read-joining in QIIME 2 tutorial Alternative methods of read-joining in QIIME 2 — QIIME 2 2018.2.0 documentation until Sequence quality control step then using deblur.
I just got worried because almost all my reads are retained, here it attached my qzv file.
crassa-demux-joined-filter-stats.qzv (1.2 MB)
qiime vsearch join-pairs
--i-demultiplexed-seqs A_crassa-demux.qza
--o-joined-sequences crassa-demux-joined.qza
qiime demux summarize
--i-data crassa-demux-joined.qza
--o-visualization crassa-demux-joined.qzv
qiime quality-filter q-score
--i-demux crassa-demux-joined.qza
--o-filtered-sequences crassa-demux-joined-filtered.qza
--o-filter-stats crassa-demux-joined-filter-stats.qza
qiime metadata tabulate
--m-input-file crassa-demux-joined-filter-stats.qza
--o-visualization crassa-demux-joined-filter-stats.qzv
My question:
Why my joined reads are not connected in the interactive quality plot of my file crassa-demux-joined.qzv
crassa-demux-joined.qzv (295.2 KB)
Thanks in advance for your guidance