RNASeq Differential Expression Analysis.

Project description

Comparative transcriptome profile of genes differentially expressed in longissimus dorsi muscles between Japanese black (Wagyu) and Chinese Red Steppes cattle by RNA-seq

Data Description.

RNAseq samples from two cattle breeds i.e, Japanese black (Wagyu) cattle and Chinese Red Steppes cattle.

Sample- Breed

SRR13107018- Japanese black (Wagyu) cattle

SRR13107019- Japanese black (Wagyu) cattle

SRR13107020- Japanese black (Wagyu) cattle

SRR13107021- Chinese Red Steppes cattle

SRR13107022- Chinese Red Steppes cattle

SRR13107023- Chinese Red Steppes cattle

*** For practise, you can obtain the fastq files from NCBI SRA website using the fastq-dumpcommand from the SRA Toolkit to download the data in FASTQ format and store it in the Data folder.

RNASeq anaylsis workflow.

The RNAexpression.sh script.

This script is a pipeline for RNA-Seq data analysis, and it includes quality control, alignment to a reference genome, transcript assembly, and abundance estimation.

The RNAexpression.sh Script Input:

Fasta files

The RNAexpression.sh Script output:

The abundance estimation files for each sample will be stored in the ballgown folder within the Data folder. Theses will serve as an input for the R script

The RNASeq.R Script.

This script is used to analyze RNA-Seq data for differential expression between different breeds of cattle. It filters the data, performs statistical tests, and then creates visualizations (plots and heatmaps) for the results.

The RNASeq.R Script Input:

ballgown folder having the abundance estimation files.

The RNASeq.R Script output:

Results plots folder containing Visualization plots heatmaps.