Sample number for galaxy mothur

1

Hi everyone,
I have one query regarding the samples number when using mothur tool. I have used mothur for 16s metagenomics data analysis for 46 samples, 2 samples and 4 samples by following the tutorials. For visualization I have used the Phyloseq R using biom file. My query is-
I am getting the classification at genera level only. I am not able to search for species level. In phinch tool and Phyloseq. it only displays genera level. So, where I can find the distinct or specific species found in the samples.
Secondly, I get black shades in abundance bar plots, even after filtering. How it can resolved.
Thirdly, if I am comparing between groups containing different number of samples, the classification could be uneven. Do I need to take same samples number in all groups. so uniformity in the data will result in good classification.

Please help me out.
Thanks
Shweta

2

For this one, it could be that your sequences are not able to be classified more specifically. You can check what the Silva reference contains here → https://www.arb-silva.de/

You can share an example if you want to for this.

You could examine the relative classification differences (percentages) instead of the absolute numbers (counts), yes?

Hope this helps @Shweta.203 ! I see your other question and will be answering that next.