BI231 NGS Data Analysis
From Bioinformatics.Org Wiki
This course teaches biologists how to analyze data from Next Generation Sequencing (NGS) platforms. Topics to be covered include the description of sequencing strategies and platforms, experiment types, data formats, and command line tools for various workflows, such as quantification of transcripts, alternative splice forms, copy number variants, single nucleotide polymorphisms, etc.
The course is divided into 4 sessions, Monday through Thursday, with Friday as a reserve day. Homework assignments will involve running computationally intensive tools.
- Session 1
- What is Next Generation Sequencing, and how is it different from traditional sequencing?
- Various NGS technologies/platforms, experiment types and applications
- Workflows for various NGS experiments
- Session 2
- Steps involved in implementing various NGS workflows (variant discovery, expression profiling, etc.) - working with reads, alignments, quality scores, etc.
- Algorithms and tools for NGS read alignment, SNP calling, etc.
- Various file formats such as SAM, VCF, BED, WIG, PILEUP, etc.
- Session 3
- Four different workflows for mutation discovery (CrossBow, Bowtie, BWA, MAQ)
- Variant effect prediction on genes
- Functional consequence of gene product variation (GO, SIFT, POLYPHEN)
- Session 4
- TopHat and Cufflinks for RNA-seq
- Finding novel transcripts
- Expression of splice variants
Course attendees should have access to a powerful Linux/Unix workstation to run the examples in this course. Minimum requirements: Dual-CPU, quad-core 2 GHz processor or higher, 32 GB RAM, 200 GB free disk space. Attendees can optionally subscribe to our server for 1 month for an additional $50 lab fee.
If you are interested in an upcoming course, register using instructions below. (Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues.)
- Step 1
- If you haven't already done so, create an on-line account to access the educational section of our website. Please note that the registration for our educational system is separate from that of the main website; you will require another account.
- Step 2
- Register for the course by making a payment using either the on-line registration form (click on the name of the course where it appears in the list of upcoming courses; use this form only for PayPal payments and credit card payments via secured PayPal), or by sending in the registration form (PDF; use this form if paying by US checks, credit card or corporate purchase order).
Please also check the course tuition rates and discounts.
Registration deadline: When full
Tuition & discounts
- Live instruction held on-line
- For-profit & government: $1,000 USD
- Non-profit & self-pay: $600 USD
- Live instruction held on-site
- For-profit & government: $1,200 USD
- Non-profit & self-pay: $800 USD
- On-demand instruction held on-line
- For-profit & government: $600 USD
- Non-profit & self-pay: $400 USD
Additional discounts are available as follows:
- Professional members: 20% discount
- Limited scholarships may also be available for those residing in low-income economies (please inquire).
The necessary software, lecture notes and exercises will be provided.
Live instruction held on-line
On-line/live courses use the WebEx on-line meeting system. Access information will be provided prior to the start of the course. Unless otherwise noted, each lecture begins at 16:00 GMT and runs for about two hours, depending on the topics covered.
For those who cannot attend the lectures at those times, the lectures will be recorded and placed on the course website as AVI video files each day, within one day. Students will also be able to communicate with the instructor and other students via the course forums. Lecture attendance is therefore not required.
Since this will be an interactive, hands-on workshop, all attendees will need a computer with a broadband Internet connection (1 Mbps or faster is strongly recommended for those watching the live lecture), a sound card with speakers, a modern Web browser, and Java. A microphone and webcam are not required but may be used.
This course is certified by the Bioinformatics Organization, Inc., the largest international affiliation in the field, and it will count as 6 "Continuing Scientific Education" (CSE) units (one unit per contact hour) within the Organization. Students completing the course will receive a certificate attesting to that.
For any course type, if a student is not satisfied with the conduct or content of a course, they may request a full refund within the first two days of lecture. After two days but within a week, a 50% refund will be granted. After one week, a 100% credit toward another course will be granted. No refunds or credits apply beyond those stated here.
Please contact us for questions or additional information.