Hands on Training Program on Transcriptome-Seq Data Analysis Quality Control, Read Mapping, Visualization and Downstream Analyses
What is in focus?
Day: 1
Morning Session (10:00 AM-1:00 PM)
- Linux for Bioinformatics : Introduction to the command line and important commands
- Combining commands by piping and redirection
- Introduction to bioinformatics file formats and databases
- Usage of important bioinformatics toolkits
- Introduction to R
Afternoon Session (2:00 PM-5:00 PM)
- NGS data types, File formats,
- Understanding raw data on NGS
- Lecture on data quality check and filtering
- Data QC practical session
Day: 2
Morning Session: (10:00 AM-1:00 PM)
- Lecture on workflow of denovo transcriptome assembly
- Read mapping/alignment to reference genome, with Bowtie and Tophat
- SAM tools an SAM Alignment formats
- Mapping/ Alignment of reads to reference practical session
Afternoon session (2:00 PM-5:00 PM)
- Transcript identification and annotation
- Differential gene expression
- Graphical representation of differentially expressed genes using CummeRbund
- Report generation, Recap of workshop
- Clarifying doubts
What is the benefit of this workshop?
This workshop will provide an introduction to Next Generation Sequencing (NGS), platforms, data generation, data analysis and tools for quality check, read alignment/ mapping, differential gene expression.This workshop will be delivered using a mixture of lectures and computer based hands-on practical sessions using real data. Participants and speakers will share successful experiences and exchange ideas in order to implement and establish new workflows.
Target Audience & Prerequisite:
M.Sc students, PhD students, postdocs, research staff and junior faculty members who are interested in, or already working with, next-generation sequencing data are more than welcome. No programming experience is required, although working experience under Linux command-line environment will be highly beneficial. For applicants that lack this knowledge, we will provide a brief introduction and a warm-up practice.
Registration Start: 01 June, 2017
Last Date for Registration: 26 June, 2017
Course Fees: 2000/- Only
Registration Procedure:
The interested participants are required to fill the registration form along with 2000/- Course fees by check in favour of the "Clovergen Life Sciences Pvt Ltd" payable at Bangalore.
Selected candidates will be intimated by 27 June, 2017.
Laptop and Equipments Participants should bring a laptop with WiFi support able to boot from USB keys. In case we fail to boot your computer into Linux from the USB keys, you will need to agree to install aVirtualBox and run Linux UBUNTU from within your current operating system. Instructions and software will be provided at the workshop. Note that you need at least 500 GB of free disk space and at least 4 GB of memory (RAM) for this option, and that you can safely and completely remove the software after the course. (Note: If the student is not having a Laptop, We will provide the working computer to get practice)
Venue and Tentative Places Clovergen Life Sciences Pvt Ltd, Bioinformatics Laboratory IABT, University of Agricultural Sciences, Dharwad-580005
Speakers Bioinformatics, Programming & Genomics Group from Clovergen
Office Address Clovergen Life Sciences Pvt Ltd
165, 4th Main, 2nd B Cross, Talakavery Layout, Amruthahalli, Bangalore-560092
Incubation Center Room No: 3, KBITS Facilitation Center, Institute of Agri-Biotechnology (IABT), University of Agricultural Sciences, Dharwad-580005 Email: clovergenls@gmail.com Tel.No: +91-9844158444
It will be helpful if you can introduce the trainers. We hope those people would be experts in this area. Name, designation, education, area of expertise and years of experience will be very helpful to decide.