*** I am asking this question for third time, previously someone answered the question incorrectly and with the same theoretical explanation

The person who answered this question previously, PLEASE DO NOT ANSWER THIS QUESTION IF YOU DON'T KNOW about Galaxy software.

Only person who has expertise using Galaxy software, please answer it. Galaxy software is available at https://usegalaxy.org/

Please carefully read below question and provide all details, so that person can follow those steps in Galaxy to reproduce those analysis.****

Now here's the question:

Next-Generation Sequencing has fostered a revolution in bioinformatics, opening the pathway to understanding biology in ways only previously imagined. Through the combination of millions of small sequences extracted and enumerated, the biology of the system can be probed and interrogated in very precise ways.

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

QC analysis of an RNA-SEQ NGS dataset using FASTQC

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

Generate statistics for your BAM dataset using SAMTools Stats

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