Standardization of de novo and reference workflow for RNA-SEQ data
Student name: Ms Mita Samanta
Guide: Dr Pallavi Somvanshi
Year of completion: 2017
Host Organisation: Jawaharlal Nehru University, New Delhi
Supervisor (Host Organisation): Dr Andrew M. Lynn
Abstract: The emergence of Next Generation Sequencing (NGS) platforms has led to the resurgence of research in genomics. NGS being a high throughput technology revolutionised the sequencing of DNA and RNA, making it more rapid, efficient and precise as compared to its other counterparts – Sanger sequencing and Microarrays. This project deals with analysis of NGS data using the local instance of Galaxy (a web-based, open source platform) called NGSAP (Next Generation Sequencing Analysis Pipeline) which runs on the local server and can be downloaded easily by anyone. The standalone method of NGS data analysis requires prior knowledge of computer language and coding, therefore workflows (both de novo and reference based) were developed and tested in this project so that it could be easy for biologists to analyse transcriptomics data without any prior computer knowledge.
Each workflow is divided into three major parts i.e. Assembly, Annotation and Differential expression for both De novo as well as Reference based assembly. Major focus is on testing out these workflows to check its efficiency and whether or not a real data can be analysed using them. In this project, computer generated test samples were used to check the working and efficiency of the developed workflows. Also, samples from organism X were analysed using de novo workflow.
If successful, these workflows can be used for identifying transcripts, characterizing transcript’s structural complexity and coding content and even understanding which genes and isoforms are expressed in different samples (tissues, environment conditions, etc.) for both model and non-model organisms.
Key words: NGS analysis, NGSAP, workflow, Assembly, Annotation, Differential expression
