Nanopolish-call-methylation-0.10.2
- amcooksey (Unlicensed)
Owned by amcooksey (Unlicensed)
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
- Resources: https://github.com/jts/nanopolish
Test Data
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