The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Nanopolish-call-methylation-0.10.2

This App runs Nanopolish (version 0.10.2) to 

  • Classify nucleotides as methylated or not.

App Creator

Amanda Cooksey

Quick Start

  • Nanopolish 0.10.2 takes the following files as inputs
    • FASTA or FASTQ reads file of basecalled nanopore reads
    • Folder of FAST5 files corresponding to your FASTA/Q file
    • Index files generated with Nanopolish index 0.10.2
    • BAM alignment file of reads
    • BAM index file
    • FASTA genome file

Test Data

Icon

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> nanopolish -> call_methylation

Input File(s)

  • FASTA or FASTQ reads file of basecalled nanopore reads
  • Folder of FAST5 files corresponding to your FASTA/Q file
  • Index files (4) generated with Nanopolish index 0.10.2
  • BAM alignment file of reads
  • BAM index file
  • FASTA genome file

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the section below.

Leave all parameters as default.

Output File(s)

The output of call-methylation is a tab-separated file containing per-read log-likelihood ratios (positive values indicate more evidence for 5-mC, negative values indicate more evidence for C). When run with the above parameters the app will generate an output file called call_methylation_output.txt

Tool Source for App

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