Low Feature Count noticed after qiime feature-classifier classify-sklearn

[cherman2 (Chloe Herman)]

Hi @divyaprince321
These are really good resources for this

Merging, Quality control and overlapping

Hello to everyone. I have some questions related to qiime2 and I would appreciate it if you can help me out please. First of all, I have to say that one part of my question is similar to an old post in qiime forum (problem with merging step in qiime2 with dada2) but since those explanations weren’t clear for me I will ask again. I try to give details as much as I can. I am analyzing the 16S data and I have 48 paired-end samples. The primers are: 16S-341F and 16S-805R. The questions are : 1-…

Questions about V3–V4 primers for 16S rRNA amplicon sequencing, and calculating overlap

Hi there, I’ve got some questions about primers and about calculating overlap for paired-end reads. I hope I’m posting in an appropriate place. Sorry, if not. This is my first post. Background: We’ve done some 16S rRNA amplicon sequencing with primers that Illumina says are used to sequence the V3 and V4 variable regions of the 16S rRNA gene. The Illumina guide can be found here. Forward primer: 5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG-3’ Reverse primer: 5’-GTCTCGTGGGCTCGGAGA…

I am not quite sure why your sequences are not merging because it seems like there is enough overlap between sequences.

Are you sure that there are no primers in your sequences?

[divyaprince321 (divya)]

Hi @ cherman2
Not much sure about the primer removal, just guessing it that the sequencing was outsourced so the agent may have demultiplexed.
Anyways I have received the primer details
16S Amplicon PCR Forward Primer:
5'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG3’
16S Amplicon PCR Reverse Primer:
5'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC3’
Will try using these and seek what comes out.
Thanks