How can I use rdp classifier method when use pick_open_reference_otus.py

Hi, Everyone

I am new in use Qiime software to analysis 16S-sequencing data. When I use pick_open_reference_otus.py and want to use rdp classifier method to pick otus, but the default method is uclust, I don't know how to set the parameter.

Someone can help me? Thank you very much.

qiime

• 1,939 views • link

updated 3.4 years ago by Ram

• written 9.2 years ago by bioxujintian •

0 answers

No answers yet.

More posts like this

QIIME2 Vs MetaPhlAn3
written 4.3 years ago by Abhishek •

Hi all, I have been going through documentation for Qiime and Metaphlan and am trying to understand the difference between the two. I do understand …
How to predict new data using NMF classifier
written 6.1 years ago by a511512345

Hello there, I am doing NMF analysis using NMF package. When I built a new NMF classifier, I did not know how to predict new …
The problem about tophat software -G parameter
written 8.3 years ago by Wayne Lee •

Holle everyone! I am a beginner in RNA-Sequencing. I have a simple problem about 'tophat' software: what different on result between using -G parameter and …
16S rRNA de novo otu picking analysis
written 8.4 years ago by dcron13 •

I have been attempting to create a 16S rRNA analysis pipeline that uses de novo otu picking, using mostly Qiime. The pipeline that I am …
importing UBAM files to QIIME 2.0
written 8.5 years ago by osamashehzad.786 •

Hello everyone! I am new to fields of bioinformatics and trying to learn it as much as possible. I used iontorrent to sequence 16s rRNA …
Error: assigin taxonomy, pick_open_reference_otus.py
written 9.7 years ago by ericleelionking •

Dear expert in qiime, Hello. I am a qiime newbie. I am using qiime trough virtual box. After split libraries,I used a script "**pick_open_reference_otus.py -i …
Inconsistent among simpson index curve and shannon index curve in alpha diversity analysis using QI…
written 9.7 years ago by Ginsea Chen

Dear all ---------- I have used qiime to pick OTUs from 16s DNA datasets with 5 samples. Singletons OTUs have been filtered with -n 2 …
16S sequencing analysis: from fasta to otu to PCA&Heatmap
written 9.9 years ago by shlomsauce •

Hello, I'm sort of new to all bioinformatic tools and analysis and I've been assigned to a project involving 16S RNA sequencing analysis. *Long story …
Phyloseq biom input
written 10.3 years ago by xuling2015 •

Hi Everyone, I'm doing 16S sequencing data analysis. After itagger software cluster. I got a biom file. Then I'm trying to import biom file to …
What Is The Best Pipeline For 16S Rna Metagenome Analysis?
written 15.7 years ago by Pawel Szczesny

<p>I'm doing lots of analysis on sequencing of 16S RNAs by 454. In addition to self-made tools I've used MEGAN quite extensively and plan to …