Introduction

Accession: PRJNA657899

This example dataset contains RNA-Seq reads that have been mapped (STAR) to their genome (Gallus gallus). Some obtained BAM files together with the latest structural annotation (GFF) are provided here to show an exemplary usage of “BAM Quality Control” 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

Original Data

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

• https://www.ncbi.nlm.nih.gov/bioproject/PRJNA781819

  • Convenient website to download the files from NCBI https://sra-explorer.info/#

• Genome: 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: 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

Bioinformatic Analysis

1- Analysis Step

Application

Bam File Quality Control

Input

• Input BAM files

  • 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

srr1699076.box