KBase Documentation
  • KBase Documentation
  • KBase Terms & Conditions
  • Getting Started
    • Signing Up and Signing In
      • Step-by-Step Sign Up
    • Supported Browsers
    • Narrative Quick Start
    • Narrative Interface User Guide
      • Access the Narrative Interface
      • Tour the Narrative Interface
      • Narrative Navigator
      • Create a Narrative
      • Explore Data
      • Add Data to Your Narrative
      • Browse KBase Analysis Tools
      • Analyze Data Using KBase Apps
      • Job Browser
      • Revise Your Narrative
      • Format Markdown Cells
      • Share Narratives
      • Linking Static Narratives to ORCID
      • Access and Copy Narratives
      • Organizations
    • FAQs
  • Manage Your Account
    • Linking Accounts
    • Linking KBase to ORCiD
  • Working with Data
    • Data Upload and Download Guide
      • Data Types
      • Importing Data
        • Bulk Import Limitations
      • Assembly
      • Genome
      • FASTQ/SRA Reads
      • Flux Balance Analysis (FBA) Model
      • Media
      • Expression Matrix
      • Phenotype Set
      • Amplicon Matrix
      • Chemical Abundance Matrix
      • SampleSet
      • Compressed/Zipped Files
      • Bulk Import Specification
      • Downloading Data
    • Searching, Adding, and Uploading Data
    • Filtering, Managing, and Viewing Data
    • Linking Metadata
      • Ontologies and Validated Terms
    • Public Data in KBase
    • Transfer Data with Globus
  • Using Apps
    • Analysis Apps in KBase
      • Assembly & Annotation
      • Comparative Genomics
      • Metabolic Modeling
      • Metagenomics & Community Exploration
      • Data Matrices - Amplicon, Stats
      • Chemical Abundance
      • Expression & Transcriptomics
    • Apps in Beta
  • Running Common Workflows
    • Assembling & Annotating Microbial Genomes
      • FAQ: Assembly and Annotation
    • Comparative Genomics & Phylogenetic Analysis
      • FAQ: Comparative Genomics
    • Metagenomic & Community Analysis
      • FAQ: Metagenomics & Community Analysis
    • Transcriptomic Analysis
      • FAQ: RNA-seq Analysis
    • Constructing Metabolic Models
      • Constructing and Analyzing Metabolic Flux Models of Microbial Communities
      • FAQ: Metabolic Modeling
  • Community Developed Workflows and Tools
    • Functional Annotation
    • Functional and Taxonomic Profiling of MAGs
    • Taxonomy
    • Viral
    • Random Walk with Restart Toolkit
  • Troubleshooting
    • Problems with the User Interface
    • Help Board
    • How to Report Issues
    • Job Errors and Their Meanings
      • Common Job Errors
        • The Job Log
      • Import Job Errors
      • Assembly App Errors
      • Annotation App Errors
      • Functional Genomics App Errors
      • Modeling App Errors
  • Developing Apps
    • The KBase SDK
    • Create a KBase Developer Account
    • KBase GitHub Repository
  • External Links
    • KBase Narrative Interface
    • KBase web site
    • KBase App Catalog
  • kbase.us
Powered by GitBook
On this page
  • What does the tail <1% each taxon mean in the Kaiju output?
  • Can I use the GTDB database within Kaiju?
  • Does the Kaiju analysis give a text output that can be used in R, for example?

Was this helpful?

  1. Running Common Workflows
  2. Comparative Genomics & Phylogenetic Analysis

FAQ: Comparative Genomics

What does the tail <1% each taxon mean in the Kaiju output?

This option allows users to exclude rare lineages which would congest the plot. However, underlying analysis is not affected and the data can be replotted.

Can I use the GTDB database within Kaiju?

Yes, you can run the our GTDB-tk Classify app on the same data as you run through Kaiju and compare. The GTDB-tk app is in the Microbial Communities section of the Apps Panel in the Narrative interface. One distinction: Kaiju runs on raw sequencing data (reads) and GTDB-tk works on assembled contigs.

Does the Kaiju analysis give a text output that can be used in R, for example?

Yes, at the bottom of the App cell you can see an option to download kaiju_classification.zip and kaiju_summaries.zip which both contain text files.

PreviousComparative Genomics & Phylogenetic AnalysisNextMetagenomic & Community Analysis

Last updated 4 years ago

Was this helpful?