---
title: "RNA-Seq BAM File Quality Control with RSeQC (Gallus gallus)"
canonical: "https://help.biobam.com/space/OED0324/3525083475/RNA-Seq%20BAM%20File%20Quality%20Control%20with%20RSeQC%20(Gallus%20gallus)"
format: markdown
---
# Introduction

This example dataset includes RNA-Seq reads that were aligned to the *Gallus gallus* genome using STAR. A set of BAM files, along with the latest structural annotation (GFF), is provided to illustrate the use of the **BAM Quality Control **tool in OmicsBox.

### Dataset description

Information about the experiment.

- RNA-Seq
- 12 samples
- HiSeq 2000
- Paired-End

### Publication

[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7936876](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7936876/)

### Original Data

Link to the public repositories where the original data can be found:

- [NCBI Bioproject](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA781819).
- [Genome FASTA file](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b_genomic.fna.gz).
- [Annotation GFF](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b_genomic.gff.gz).

> ℹ️ [SRA Explorer](https://sra-explorer.info/#) is a convenient website to easily download raw sequencing data from NCBI.

# Bioinformatic Analysis

## 1- Analysis Step

### Application

[BAM File Quality Control.](https://biobam.atlassian.net/wiki/spaces/OBD/pages/3044212737)

### Input

- [Input BAM files](https://drive.google.com/drive/folders/1FSj9KZg62qfFb_p-UNc1-n4U-DemdDwg?usp=drive_link)
  - 2 samples have been selected and further reduced in size (samtools view -bo subset.bam -s 123.1 alignments.bam chr1 chr2).
- [Annotation file (Gene Model)](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b_genomic.gff.gz).
  - GFF has to be extracted before providing it.

### Parameters

- Default values
- Provide the Annotations mentioned above
  - Extract the GFF before providing it

### Execution Time

- 8:00 for the 2 samples and annotations provided

### Output