# RNA-Seq-1

**Repository Path**: mayu95/RNA-Seq-1

## Basic Information

- **Project Name**: RNA-Seq-1
- **Description**: RNA-Seq Workflow Based on Snakemake and Conda
- **Primary Language**: R
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 1
- **Forks**: 1
- **Created**: 2021-06-29
- **Last Updated**: 2022-08-02

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# RNA-Seq Workflow Tutorial

### 1. Make project directory
```
# the project directory contains specific GROUP name and current DATE
GROUP=XXX
DATE=`date +"%Y%m%d"`
mkdir ~/Project/${GROUP}_${DATE}
```

### 2. Clone the repository
```
cd ~/Project/${GROUP}_${DATE}
git clone https://github.com/bioxfu/RNA-Seq
cd RNA-Seq
```

### 3. Copy/Download the raw data
```
DATAPATH=/the/path/of/the/raw/data/on/HPC

# if you are working on the HPC, copy the raw data
./script/copy_rawdata.sh $DATAPATH

# if you are working on the local machine, download the raw data
./script/copy_rawdata.sh $DATAPATH --download
```

### 4. Rename the raw data
```
# dry run to check if mv command is correct
./script/rename_rawdata.sh --dry-run

# then do it 
./script/rename_rawdata.sh
```

### 5. Create *config.yaml* and *Snakefile* based on the examples
```
cp example/example.HPC.plant.config.yaml config.yaml
cp example/example.plant.Snakefile Snakefile
cp example/example_design_table.tsv design_table.tsv

# edit config.yaml and design_table.tsv
```

### 6. Initiate the project
```
source init.sh
```

### 7. Dry run the workflow to check any mistakes
```
./dry_run.sh
```

### 8. Run the workflow
```
# if you are working on the HPC
./run_HPC.sh

# if you are working on the local machine
./run.sh

# check the workflow progress in nohup.out file
tail nohup.log 

# check the jobs on HPC
qstat

# to delete all the jobs at once
qselect -u <username> | xargs qdel

# if you get the error: Directory cannot be locked.
snakemake --unlock 
```

### 9. Remove the temporary files
```
./clean.sh
```

### 10. Remove unwanted variation from RNA-Seq data
```
## remove batch effect using RUV
/cluster/home/xfu/R/3.5.1/bin/Rscript script/RUVSeq.R
```