After assigning taxonomy, I constructed phylogenetic tree using phangorn R package, and started prevalence filtering. But the abundance graph is not like Figure 3. I found that phangorn is not good for the large taxa (5238 taxa in my data), so I also tried RAxML to construct the tree (https://github.com/benjjneb/dada2/issues/88).
But the result is same as above. How can I make a abudance graph like figure 3?
Let me know if I'm being unclear or you need more info.
Hello,
I'm following the "Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses [version 2; referees: 3 approved]" to analyse my 454 sequence data. I followed DADA2 pipeline tutorial (https://benjjneb.github.io/dada2/tutorial.html) and fixed some commands according to the Q&A (https://benjjneb.github.io/dada2/faq.html).
After assigning taxonomy, I constructed phylogenetic tree using phangorn R package, and started prevalence filtering. But the abundance graph is not like Figure 3. I found that phangorn is not good for the large taxa (5238 taxa in my data), so I also tried RAxML to construct the tree (https://github.com/benjjneb/dada2/issues/88).
But the result is same as above. How can I make a abudance graph like figure 3? Let me know if I'm being unclear or you need more info.
Thank you,
Chaewon