Deblur reads not joined?

[Sabrin (Abdelghany)]

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

[lizgehret]

Hi @Sabrin,

Apologies for the delay in response on this!

@Sabrin

My question:
Why my joined reads are not connected in the interactive quality plot of my file crassa-demux-joined.qzv

This is most likely because you are looking at different sequences - you can also see a read separation in the interactive quality plot from our tutorial data:

I don't see anything that's glaringly problematic or concerning on my end - but please feel free to follow up if you have any additional questions or concerns!

[lizgehret]

Hi @Sabrin,

I just wanted to circle back on this - here is a great Github issue thread that discusses this 'flatlined' region you are seeing in your quality plot in greater detail. It is nothing to be concerned with, and in fact is showing the region of overlap between your forward and reverse reads. Hope this helps!