# BEguider

**Repository Path**: gaojingjing123/beguider

## Basic Information

- **Project Name**: BEguider
- **Description**: design sgRNA for ABE7.10-NGG and BE4-NGG
- **Primary Language**: Python
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 1
- **Forks**: 0
- **Created**: 2022-01-19
- **Last Updated**: 2022-10-14

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# BEguider

#### 介绍
design sgRNA for ABE7.10-NGG and BE4-NGG


#### 安装环境

利用conda进行安装


```
conda create -n beguider  --file requirements_BEguider.txt
conda activate beguider 

```


#### 输入文件实例
Examples:
        1) use genes as input file:
                Genes,Seqs
                BRCA1,TGGCTGAAGAATTTGCTAAGCAATCAGGAAAGCTGGTGG               
                ARID1A,CTCCACCGAAGGGAGGACCCACTGCCCCCAGCCGGGGTCTCG

        2) use chromosomes and coordinates as input file:
                Chrom,Coordinate,Type
                chr1,145634,r
                chrX,87632,a

        3) use rsIDs as input file:
                SNP,Type
                rs5297,r
                rs12603332,a 


#### 使用说明


```
python BEguider.py -h
usage: BEguider.py [-h] (-g GENES | -c CHROMOSOME | -s RSID) -b BASEEDITOR [-f OFFTARGET]
                   [-m MISMATCH] [-o OUTPUT]
 
    Program: BEguider
    Version: 0.1
    Author : Jingjing Gao
    Email  : <gaojingjing@ibms.pumc.edu.cn>

Optional Arguments:
  -h, --help            show this help message and exit
  -g GENES, --genes GENES
                        A txt file including genes and sequences separated 
                         by comma(,).
  -c CHROMOSOME, --chromosome CHROMOSOME
                        A txt file including chromosomes, coordinates and
                         genetic type separated by comma(,). Genetic type: 
                         r means editing wild genes, a means editing mutant 
                         genes.
  -s RSID, --rsID RSID  
                         A txt file including rsID and genetic type separated 
                          by comma(,).
  -b BASEEDITOR, --BaseEditor BASEEDITOR
                         ABE / CBE / ALL. Design sgRNA for
                           ABE(ABE7.10-NGG) or CBE(BE4-NGG) 
                           or ALL(ABE7.10-NGG, BE4-NGG)
  -f OFFTARGET, --offtarget OFFTARGET
                         True / False. True: predict off-target sites in hg38 
                           genome. (Default = False)
  -m MISMATCH, --mismatch MISMATCH
                          Allowed maximum mismatch site between sgRNA 
                           and genome while finding 
                                         off-target sites.(Default = 3)
  -o OUTPUT, --output OUTPUT
                           Output directory. (Default = current directory)
```



#### 注意事项
    如需要使用脱靶位点评估功能需从Ensembl数据库下载人参考基因组fasta文件，并放在BEguider的 Util文件夹下。
    Ensembl数据库： http://ftp.ensembl.org/pub/release-105/fasta/homo_sapiens/dna/