BI231 NGS Data Analysis

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==Objectives==
==Objectives==
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This course aims at teaching 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.
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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.
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Prerequisites: basic biology and use of command line tools. Students should contact the instructor to get a list of recommended reading materials prior to the course.
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==Instructor==
==Instructor==
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==Syllabus==
==Syllabus==
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The course is divided into 4 sessions, roughly 1-1.5 hours each. Homework assignments will involve running computationally intensive tools.
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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
; Session 1
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: Fundamentals of NGS technologies – strategies, platforms and types of experiments that can be done (whole genome, transcriptome, targeted, ChIP-Seq, etc)
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* What is Next Generation Sequencing, and how is it different from traditional sequencing?
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* Various NGS technologies/platforms, experiment types and applications
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* Workflows for various NGS experiments
; Session 2
; Session 2
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: Data formats and overview of algorithms, workflows and command line tools
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* Steps involved in implementing various NGS workflows (variant discovery, expression profiling, etc.) - working with reads, alignments, quality scores, etc.
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* Algorithms and tools for NGS read alignment, SNP calling, etc.
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* Various file formats such as SAM, VCF, BED, WIG, PILEUP, etc.
; Session 3
; Session 3
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: Whole genome sequencing workflow that is used for CNV and SNP discovery
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* Four different workflows for mutation discovery (CrossBow, Bowtie, BWA, MAQ)
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* Variant effect prediction on genes
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* Functional consequence of gene product variation (GO, SIFT, POLYPHEN)
; Session 4
; Session 4
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: Transcriptomics workflow for quantifying abundance of transcripts and alternative splicing junctions
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* TopHat and Cufflinks for RNA-seq
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* Finding novel transcripts
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* Expression of splice variants
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==Prerequisites==
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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.
{{Course footer
{{Course footer
|hours=6
|hours=6
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Latest revision as of 19:29, 4 May 2012

Contents

Objectives

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.

Instructor

Syllabus

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
Session 2
Session 3
Session 4

Prerequisites

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.

Scheduled courses

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.)

Registration

Registration for courses at Bioinformatics.Org takes two steps:

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
Live instruction held on-site
On-demand instruction held on-line

Additional discounts are available as follows:

Logistics

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.

Certification

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.

Refund policy

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.

Additional information

Please contact us for questions or additional information.

See also

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