# ARES

**Repository Path**: jumphone/ARES

## Basic Information

- **Project Name**: ARES
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2021-04-20
- **Last Updated**: 2021-04-20

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README


<img src="https://github.com/jumphone/PhenoPro/raw/master/IMG/ARES_logo_text.png" width="300">


Annotation-free toolkit for identifying RNA editing sites (ARES)

ARES is designed for detecting RNA Editing Sites (RESs) from aligned RNA-seq data.

## Notes

    Regular-RESs: RESs called from aligned reads.    
    
    Hyper-RESs: RESs called from re-aligned masked reads.
    
    When identifying regular-RESs, ARES shows much higher sensitivity than other existing tools (e.g. SPRINT). 
    
    We recommend users to use ARES and SPRINT to identify regular- and hyper- RESs, respectively.

* [Use ARES to identify regular-RESs](https://github.com/jumphone/ARES#usage)

* [Use SPRINT to identify hyper-RESs](https://github.com/jumphone/ARES#6-identify-hyper-ress-sprint)

## Requirements
    
    linux
    python3  = 3.8.2
    pysam    = 0.16.0.1
    numpy    = 1.19.1
    bedtools = v2.26.0    # https://bedtools.readthedocs.io/en/latest/
    blat     = v.36x7     # http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/

## Download ARES

    wget https://raw.githubusercontent.com/jumphone/ARES/master/ares.py

## Usage

### 1. ARES-anno

Use ARES with repeat annotation file ( **dsRNA-based part + annotation-based part with repeat annotation** )

Users can download repeat annotation file from: https://sourceforge.net/projects/sprintpy/files/dbRES/, "dbrep.zip"
    
    python3  ares.py  bam_in_path  ref_in_path  OUT_DIR  bedtools_path  blat_path  anno_in_path
    
    # bam_in_path: path to aligned reads in BAM format
    # ref_in_path: path to reference genome in FASTA format
    # OUT_DIR: ARES will generate a folder to store all results
    # bedtools_path: path to bedtools
    # blat_path: path to blat
    # anno_in_path: path to repeat annotation file. Uers can download it from https://sourceforge.net/projects/sprintpy/files/dbRES/, "dbrep.zip"
 
 
### 2. ARES-free 

Use ARES without repeat annotation file ( **dsRNA-based part + annotation-based part without repeat annotation** )
    
    python3  ares.py  bam_in_path  ref_in_path  OUT_DIR  bedtools_path  blat_path 
    
    # bam_in_path: path to aligned reads in BAM format
    # ref_in_path: path to reference genome in FASTA format
    # OUT_DIR: ARES will generate a folder to store all results
    # bedtools_path: path to bedtools
    # blat_path: path to blat


### 3. ARES-only-anno

Use ARES without dsRNA-based part ( **only annotation-based part with/without repeat annotation** )

Download "ares_onlyAnno.py"

    wget https://raw.githubusercontent.com/jumphone/ARES/master/SupFiles/ares_onlyAnno.py

Usage

    python3  ares_onlyAnno.py  bam_in_path  ref_in_path  OUT_DIR  bedtools_path  anno_in_path
    
    # bam_in_path: path to aligned reads in BAM format
    # ref_in_path: path to reference genome in FASTA format
    # OUT_DIR: ARES will generate a folder to store all results
    # bedtools_path: path to bedtools
    # anno_in_path (optional): path to repeat annotation file. Uers can download it from https://sourceforge.net/projects/sprintpy/files/dbRES/, "dbrep.zip"


### 4. Output folder

    # fc_res_dsrna.bed: RESs identified by dsRNA-based part
    # ff_res_anno.bed: RESs identified by annotation-based part
    # fg_res_all.bed: all RESs identified by ARES


### 5. Recommended alignment procedure (BWA-MEM)

bwa: http://bio-bwa.sourceforge.net/

samtools: http://www.htslib.org/download/

bamUtil: https://github.com/statgen/bamUtil
    
    # Build index
    bwa  index  -a  bwtsw  reference.fasta 
    
    # Do reads aligment
    bwa  mem  -t  cpu_number  reference.fasta  read_1.fastq  read_2.fastq  >  reads.sam

    # Sort & remove PCR duplicates
    samtools  view  -b  reads.sam  >  reads.bam
    samtools  sort  reads.bam  >  reads.sorted.bam
    bam  dedup_LowMem  --rmDups  --in  reads.sorted.bam  --out  reads.sorted.rmdup.bam  --log  log.txt 
    samtools  index  reads.sorted.rmdup.bam 
    samtools  stats  reads.sorted.rmdup.bam  >  reads.stats.txt   
   
   
### 6. Identify hyper-RESs (SPRINT)

sprint: https://github.com/jumphone/SPRINT

    samtools  view  -f4  -b  reads.sorted.rmdup.bam  >  reads.unaligned.bam
    samtools  bam2fq  reads.unaligned.bam  >  reads.unaligned.fastq
    
    sprint  main  -1  reads.unaligned.fastq  reference.fasta  OUT_DIR  bwa_path  samtools_path
    
    # Please check https://github.com/jumphone/SPRINT for the details of using SPRINT
    # when using sprint, the version of bwa should be 0.7.12, and the version of samtools should be 1.2.