NanoFreeLunch

Detecting DNA modifications quantitatively from Nanopore data without using raw signals.

Installation

1. Install Julia from https://julialang.org/. Do Not use Julia in containers like docker or singularity.
2. Enter the folder of NanoFreeLunch and type julia setup.jl.
3. The executable can be found in build/bin/, add the folder to PATH or add softlink of the executable to the folder in your PATH.

Warning: you might experience slow package downloading or get error like Exception: RequestError: HTTP/1.1 200 Connection established if Julia server connection is unstable in your region. You could change your Julia server by typing export JULIA_PKG_SERVER=https://mirrors.pku.edu.cn/julia and try again. Here is a list of alternative Julia package servers:

https://mirrors.pku.edu.cn/julia
https://mirrors.sjtug.sjtu.edu.cn/julia
https://mirrors.nju.edu.cn/julia
https://releases.tongyuan.cc/juliapkg/original

Demo

A quick demo is available at https://gitee.com/zhixingfeng/nfl-demo/tree/main/demo.

Supporting data and code

The supporting data and code to reproduce the results are available at https://gitee.com/zhixingfeng/nfl-demo.

Usage

Extracting features from aligned reads

prepdata [options] [flags] bamfile reffile locifile outdir

Args

• ``
  The model file, which is the output file of nfl train.

• ``
  The Xdata folder in the output directory of `nfl prepdata`.

• ``
  The output file (predicted modification level for qualitative detection or probability for qualitative detection).

Options

• -e, --esp <0.001>
  Precision threshold. Modification level <= esp will be set to 0, and modification level >= 1-esp will be set to 1.

• -s, --subset <"">
  Use a subset of features (default: using all the features).

• --objective
  Default is reg:squarederror. Use reg:logistic for direct regression instead of logit transformation.

Flags

• -h, --help
  Print this help message.

License

The software is under GPL3 and the data in test/data and test/results are under the CC0 public domain waiver.