DOC_ID : T11-0001
 

Doc_ID: A08-0001RDPtraset18scikit0.24.1
Editor: Anita
Reviewer: 

Description

利用RDP Classifier提供的包含RDP 分類器的參考序列和相應的分類法文件，透過q2-feature-classifier 工具來訓練適用於QIIME2分析的分類器。

Ref : https://john-quensen.com/classifying/rdp-classifier-updated/

Source

Download URL : https://sourceforge.net/projects/rdp-classifier/files/RDP_Classifier_TrainingData/RDPClassifier_16S_trainsetNo18_QiimeFormat.zip/download

File size :

1. Ref_taxonomy.txt    2.61MB 
2. RefOTUs.fa    29.5MB

Genome assemble version : bacterial and archaeal training set No.18

Detail information :

使用q2-feature-classifier version 2021.8來訓練classifiers，請確認已完成qiime2 standard analysis environment的安裝

#Activate standard analysis environment

conda activate qiime2

#移動到/work/使用者帳號資料夾

cd /work/u5777333/

#創建放置參考序列及相應的分類法文件的資料夾
mkdir RDPclassifier

#移動至資料夾

cd RDPclassifier/

#下載RDP Classifier提供的資料，解壓縮後上傳到建立的資料夾內(參考序列須先轉為大寫的序列)
 

#import data into QIIME 2 Artifacts
qiime tools import –type ‘FeatureData[Sequence]’ –input-path RefOTUs_reUpper.fa –output-path RefOTUs.qza

qiime tools import –type ‘FeatureData[Taxonomy]’ –input-format HeaderlessTSVTaxonomyFormat –input-path Ref_taxonomy.txt –output-path ref-taxonomy.qza

#Extract reference reads

qiime feature-classifier extract-reads –i-sequences RefOTUs.qza –p-f-primer GTGCCAGCMGCCGCGGTAA –p-r-primer GGACTACHVGGGTWTCTAAT –p-trunc-len 120 –p-min-length 100 –p-max-length 400 –o-reads ref-seqs.qza

#利用q2-feature-classifier version 2021.8來訓練classifiers

qiime feature-classifier fit-classifier-naive-bayes –i-reference-reads ref-seqs.qza –i-reference-taxonomy ref-taxonomy.qza –o-classifier RDPclassifier.qza

Bundle files