I'm new to sequencing and this field in general. I recently did a 16s sequencing of V4 region of a community that had unknown bacteria and Chlamydomonas reinhardtii.
The sequencing results, analyzed using DADA2, show some reads that are classified as Phylum Cyanobacteria, Class Chloroplast and Family Not assigned.
I want to know if these reads came from the Chlamydomonas reinhardtii or if there was some cyanobacteria present in the community. Please let me know if there's a way to do this?
On searching I only find ways where all chloroplast reads are discarded or there are suggestions to avoid algal chloroplast contamination during DNA extraction.
I was wondering if just discarding all chloroplast reads is the right approach if I want to know the bacterial composition? If some of the chloroplast reads came from cyanobacteria, and I discard all such reads, will I not miss the presence of cyanobacteria? What's the best way to tell if the reads are form cyanobacteria or algae?
Thanks and best regards,