BIF-30806 Group Project Group (A)rabidopsis: David Nieuwenhuijse Matthew Price Qianqian Zhang Thijs Slijkhuis Species: C. Elegans Project: Advanced.

Slides:

Advertisements

Similar presentations

Advanced ChIP-seq Identification of consensus binding sites for the LEAFY transcription factor Explain that you can use your own data Explain that data.

Advertisements

DEG Mi-kyoung Seo.

RNA-seq analysis case study Anne de Jong 2015

RNA-seq Analysis in Galaxy

NCBI resources III: GEO and expression data analysis Yanbin Yin Fall

Bacterial Genome Assembly | Victor Jongeneel Radhika S. Khetani

Before we start: Align sequence reads to the reference genome

NGS Analysis Using Galaxy

An Introduction to RNA-Seq Transcriptome Profiling with iPlant

RNA-Seq Visualization

Introduction to RNA-Seq and Transcriptome Analysis

Expression Analysis of RNA-seq Data

Transcriptome analysis With a reference – Challenging due to size and complexity of datasets – Many tools available, driven by biomedical research – GATK.

RNAseq analyses -- methods

Introduction to RNA-Seq & Transcriptome Analysis

Regulatory Genomics Lab Saurabh Sinha Regulatory Genomics Lab v1 | Saurabh Sinha1 Powerpoint by Casey Hanson.

Adding GO for Large Datasets COST Functional Modeling Workshop April, Helsinki.

An Introduction to RNA-Seq Transcriptome Profiling with iPlant.

Introductory RNA-seq Transcriptome Profiling. Before we start: Align sequence reads to the reference genome The most time-consuming part of the analysis.

Introduction to RNA-Seq

The iPlant Collaborative Community Cyberinfrastructure for Life Science Tools and Services Workshop RNA-Seq using the Discovery Environment And COGE.

Data Analysis Project Advanced Bioinformatics BIF

BIF Group Project Group (A)rabidopsis: David Nieuwenhuijse Matthew Price Qianqian Zhang Thijs Slijkhuis.

Introductory RNA-seq Transcriptome Profiling. Before we start: Align sequence reads to the reference genome The most time-consuming part of the analysis.

Galaxy – Set up your account. Galaxy – Two ways to get your data.

RNA-Seq Transcriptome Profiling. Before we start: Align sequence reads to the reference genome The most time-consuming part of the analysis is doing the.

Genome-wide association study between DSE polymorphism and Poly-A usage in Human population Hiren Karathia Sridhar Hannenhalli.

Comparative transcriptomic analysis of fungi Group Nicotiana Daan van Vliet, Dou Hu, Joost de Jong, Krista Kokki.

Bioinformatics for biologists Dr. Habil Zare, PhD PI of Oncinfo Lab Assistant Professor, Department of Computer Science Texas State University Presented.

IGV tools. Pipeline Download genome from Ensembl bacteria database Export the mapping reads file (SAM) Map reads to genome by CLC Using the mapping.

The iPlant Collaborative

Data Integration & Data Mining Tool Donald Dunbar BHF CoRE Bioinformatics Team Edinburgh Bioinformatics Meeting April 2013.

An Introduction to RNA-Seq Transcriptome Profiling with iPlant (

Comparative transcriptomics of fungi Group Nicotiana Daan van Vliet, Dou Hu, Joost de Jong, Krista Kokki.

Manuel Holtgrewe Algorithmic Bioinformatics, Department of Mathematics and Computer Science PMSB Project: RNA-Seq Read Simulation.

Transcriptomics: GeneSpring/EST integration Joe Wood.

Objectives Genome-wide investigation – to estimate alternate Poly-Adenylation (APA) usage on 3’UTR – to identify polymorphism of Downstream Sequence Elements.

Case study: Saccharomyces cerevisiae grown under two different conditions RNAseq data plataform: Illumina Goal: Generate a platform where the user will.

RNA-Seq visualization with CummeRbund

Canadian Bioinformatics Workshops

Canadian Bioinformatics Workshops

Group Medicago Basic Project: Gene expression in yeast Advanced Bioinformatics.

Canadian Bioinformatics Workshops

Microarray Technology and Data Analysis Roy Williams PhD Sanford | Burnham Medical Research Institute.

Group Medicago Basic Project: Gene expression in yeast Advanced Bioinformatics.

RNA Seq Analysis Aaron Odell June 17 th Mapping Strategy A few questions you’ll want to ask about your data… - What organism is the data from? -

Introductory RNA-seq Transcriptome Profiling of the hy5 mutation in Arabidopsis thaliana.

Canadian Bioinformatics Workshops

Case study: Saccharomyces cerevisiae grown under two different conditions RNAseq data plataform: Illumina Goal: Generate a platform where the user will.

Transcriptomics History and practice.

Introductory RNA-seq Transcriptome Profiling

Pathway Informatics 16th August, 2017

NGS File formats Raw data from various vendors => various formats

WS9: RNA-Seq Analysis with Galaxy (non-model organism )

Advanced Bioinformatics

S1 Supporting information Bioinformatic workflow and quality of the metrics Number of slides: 10.

How to store and visualize RNA-seq data

Canadian Bioinformatics Workshops

Canadian Bioinformatics Workshops

Introductory RNA-Seq Transcriptome Profiling

M. Fu, G. Huang, Z. Zhang, J. Liu, Z. Zhang, Z. Huang, B. Yu, F. Meng

Martijn Masoed Nick Rico

Pathway Informatics December 5, 2018 Ansuman Chattopadhyay, PhD

Transcriptomics History and practice.

Additional file 2: RNA-Seq data analysis pipeline

Transcriptomics Data Visualization Using Partek Flow Software

Transcriptomics – towards RNASeq – part III

Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria by Hyun Jae Lee, Athina Georgiadou, Michael.

RNA-Seq Data Analysis UND Genomics Core.

Project progress Brachypodium Rodenburg Wang Muminov Karrenbelt.

Presentation transcript:

BIF-30806 Group Project Group (A)rabidopsis: David Nieuwenhuijse Matthew Price Qianqian Zhang Thijs Slijkhuis Species: C. Elegans Project: Advanced (+Basic)

Progress Report

Project Overview Dataset Preparation Transcriptome Construction Pipeline Differentially Expressed Genes Gene Function Biological Explanation Co-expressed Genes Modules Functional Description & Explanation Module Conservation b/w species Gene Expression (Basic Project) Relationship to Transcript Properties Visualisation of Interaction Network

Results so far David Nieuwenhuijse Qianqian Zhang GeneID and GO term extraction tool Cytoscape GO enrichment analysis Finding automatic GO enrichment tool for pipeline Qianqian Zhang Create shell script for running Cuffdiff, Gffread and Samtools program Get the gene lists of most differentially expressed genes and highest expressed genes Visualization of differentially expressed genes by cummeRbund package: Density plot, Scatter plot, Volcano plot, P value distribution plot, MA plot etc. Basic statistics of differentially expressed genes

Results so far Matthew Price Thijs Slijkhuis Script for listing the top 100 expressed genes Script for determining GC-content, transcript & intron length Script for getting correlation between each transcript property and the expression level Thijs Slijkhuis Created a shell script that: Downloads the source files Converts SRA into FASTQ files Performs bowtie2-build Performs tophat Performs cufflinks Programmed a script that sorts cuffdiff output on p-value (significance in differential expression), extracts gene names from it

Issues/Challenges Co-expressed Genes Modules GO enrichment analysis WGCNA package not usable in our case Use cummeRbund package to get Heatmaps GO enrichment analysis Not many genes are annotated in the GO database. Gene id of the differentially expressed genes are not compatible with the NCBI database. Transcript sequences Not all expressed transcripts in the .gtf file can be matched to their corresponding sequence in the fasta file.

Thank you for your attention!