---
title: "Reads Demultiplexing with Cutadapt"
canonical: "https://help.biobam.com/space/OBD/3293708289/Reads%20Demultiplexing%20with%20Cutadapt"
format: markdown
---
# Introduction

 GBS sequencing of Zea mays NAM population.

### Dataset description

Illumina multiplex reads from *Zea mays*. Each sequencing read contains a barcode sequence at 5' that allow to effectively demultiplex them.

- Genomic DNA seq
- Genome Analyzer IIx System (Illumina, Inc.)

### Publication

[https://www.pnas.org/doi/full/10.1073/pnas.1413864112](https://www.pnas.org/doi/full/10.1073/pnas.1413864112)

### Original Data

- SRA Experiment: [NCBI - SRP009896](https://trace.ncbi.nlm.nih.gov/Traces/?view=study&acc=SRP009896)
- ENA: [ENA Browser - SRP009896](https://www.ebi.ac.uk/ena/browser/view/SRP009896)
- References (NCBI or Ensembl): [NCBI - 25775595](https://pubmed.ncbi.nlm.nih.gov/25775595/)

# Bioinformatic Analysis

## 1- Analysis Step​

### Application

[https://biobam.atlassian.net/wiki/spaces/OBD/pages/3356328169](https://biobam.atlassian.net/wiki/spaces/OBD/pages/3356328169) 

### Input

- [FASTQ files SRR391079, SRR391080, SRR391081, SRR391082, and Barcodes file](https://drive.google.com/file/d/1sxiF4ijqp9jHvFrPa3LWsnxtIHmA0rHJ/view?usp=sharing)

### Parameters

- Adapter Position: Beginning (5' end)
- Allowed Errors: 0
- Save Unmatched Sequences: False
- Include Sample Name: False
- File Format: .fastq.gz
- Save Counts Table: True

### Execution Time

15-20 min

### Output

- [Result files (including a report, two graphs and a tabular txt file).](https://drive.google.com/file/d/1bMaa__qp8Ij3QUO6ZIHzy5gGt_JZRUuh/view?usp=sharing)
- 96 FASTQ files containing the demultiplexed reads.