Please provide all steps starting how to get RNA SEQ file, then how to get RNA SEQ FASTQ file and then perform below analysis. All sort of details are appreciated to reproduce the analysis.

This assignment will have you execute the steps of an NGS workflow using the Galaxy system.

A. QC analysis of an RNA-SEQ NGS dataset using FASTQC

B. Mapping the NGS dataset using a alignment and mapping program BWA-MEM

C. Generate statistics for your BAM dataset using SAMTools Stats

D. Design a workflow for Variant Calling (creating a VCF file) and Annotation using programs available in Galaxy

The required deliverables for the assignment are selected to reinforce the information needed to reproduce the analysis. With either option, the work that you perform should be documented sufficient for reproduction by another individual or student. (A good way to test your approach is to have one of your peer students attempt to reproduce your results. Remember, sharing insight is permitted provided attribution is given to the source of information used.)

A written description of the analysis performed including programs and/or modules used as well as data formats

Identifiers for the datasets and their source

Statistics about your generated BAM file

A diagram of the workflow steps for the analysis you performed

A diagram of the workflow steps used to conduct variant analysis

A written description of the variant workflow including identifying programs used and data formats employed

A written discussion of challenges encountered recommendations to improve the assignment