## SCANS tutorial

### Install SCANS

Clone SCANS git repository
```
git clone https://github.com/IGDRion/scans.git
cd scans/
```

Create a new environment containing SCANS dependencies
```
bash create_SCANS_env.sh

```
To activate it
```
conda activate ./SCANS_ENV
```

Go to scans repository and export SCANSPATH variable
```
export SCANSPATH=${PWD}
export PATH=$PATH:${SCANSPATH}/bin/
```

### Test with toy dataset

```
cd toy_data/
for i in sequence/*gz; do tar -xzvf $i; done

# format gtf input data (orthology files already formatted)
format_input_files.sh --config config.txt --output .

# synteny analysis method 1
perform_synteny.sh --config config.txt --output . --orthology orthology --synteny method1

# synteny analysis method 2 (could take few minutes)
perform_synteny.sh --config config.txt --output . --orthology orthology --synteny method2

# sequence alignment analysis method 3
perform_seq_alignment.sh --config config.txt --output . --biotype lncRNA --coverage 0.5
```

Once all analysis are done, you can perform the additional analysis: data summary and visualization.

```
# to get summary of all methods for one species 
process_output_results.sh --summary --species ectosp7 --resultsDir scans_results

# to visualize one-to-one orthologous lncRNAs by species pair
process_output_results.sh --upsetPlot byPair --species ectosp7 --resultsDir scans_results --config config.txt --species2 esubulatus

# to visualize one-to-one orthologous lncRNAs by method
process_output_results.sh --upsetPlot byMethod --species ectosp7 --resultsDir scans_results --config config.txt --method met1
```