Dear Whom It May Concern,
I just wanted to double check that I am running deblur correctly and how to interpret the stats that are given to know why I lost a good chuck of my sequences.
I am using the 515-806 primers from EMP, trimmed the primers and to max length of 250 using trim-galore and fastx, then went to QIIME2
I ran the quality filtering script as follows
qiime quality-filter q-score-joined
--o-filtered sequences reads_trimmed_joined_filtered.qza
Sequences went from 14,560,145 to 14,556,787 with that run (visualization attached). Based upon that visualization I chose a trim length of 242 when my minimum length was 243 according to the visualization. Then I ran the following script for deblur
qiime deblur denoise-16s
I went from 14,556,787 to 5,713,447 sequences (table visualization too big to attach). I am unsure how to interpret the deblur stats visualization (attached) in order to find out why my sequences were dumped. I would appreciate any assitance in interpreting it as well as indicating if I did anything wrong to lose so many sequences.
Thank you for your time and help.