README.md

# NET-seq Pipeline

## REQUIREMENTS
- bedtools
- curl
- python 2.7, moduls:
    - HTSeq
    - pysam
- R
- samtools
- STAR (2.5.3a)
- wget
- bzip2 or gzip if file is compressed, respectively

## STEPS
1. Molecular Barcode Extraction
2. Reads mapping (both sets: with and without barcodes)
3. Reverse transcriptase mispriming events removal
4. Recording of the 5' end position (3' end position of the original nascent RNA)
5. PCR duplicates removal
6. Removal of sequencing reads due to splicing intermediates

## USAGE
1. Fill in the parameter files: parameter_dependencies.in and parameter_template.in
2. Make the file runNetSeqPipe.netPipe executable
    chmod -x runNetSeqPipe.netPipe
3. Run the runNetSeqPipe.netPipe file
    bash runNetSeqPipe.netPipe