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Course Syllabus-Coursera Transcriptomics

This course focuses on bioinformatics methods for analyzing RNA sequencing data, covering both short and long read sequencing techniques. It includes four modules that address gene expression analysis, differential splicing, transcriptome reconstruction, and differential expression, utilizing various tools and providing hands-on instruction. Students are assessed through weekly quizzes and must achieve a minimum final grade of 70% to pass, while also adhering to academic integrity standards regarding plagiarism.

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11 views

Course Syllabus-Coursera Transcriptomics

This course focuses on bioinformatics methods for analyzing RNA sequencing data, covering both short and long read sequencing techniques. It includes four modules that address gene expression analysis, differential splicing, transcriptome reconstruction, and differential expression, utilizing various tools and providing hands-on instruction. Students are assessed through weekly quizzes and must achieve a minimum final grade of 70% to pass, while also adhering to academic integrity standards regarding plagiarism.

Uploaded by

Sajad
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Course description

This course will cover bioinformatics methods for analyzing transcriptomic RNA sequencing data
generated with the short read (RNA-seq) and long read (PacBio, ONT) sequencing. In its four
modules, the course addresses the core transcriptomics questions: What are the genes and
transcripts expressed in a given sample or condition of an experiment?, What are their
expression levels?, and What are the differences in gene expression and splicing patterns
between conditions? It provides hands-on instruction on how to use popular and/or emerging
tools such as STAR, PsiCLASS, DESeq2, rMATS, MntJULiP, Minimap2 and IsoQuant. This is an
intermediate level course, and assumes basic knowledge on using command line bioinformatics
tools in a Unix-type environment.

Course Content

M1. Gene expression analysis with RNA-seq


• Spliced alignment: STAR
• Transcript assembly: PsiCLASS
• Differential gene expression: Cuffdiff2, DESeq2

M2. Differential splicing analysis with RNA-seq


• Types of tools
• Isoform-level: Cuffdiff2
• Event-level: rMATS
• Intron-level: MntJULiP, IRFinder
• Visualization: IGV, Jutils

M3. Transcriptome reconstruction with long RNA reads


• Alignment: Minimap2
• The FLAIR pipeline: correct-collapse-quantify
• The IsoQuant pipeline: aggregate-correct-enumerate-quantify

M4. Differential expression and splicing analysis with long RNA reads
• Differential abundance versus differential usage
• Short read tools: DESeq2, drimSeq
• Long read tools: LIQA

Weekly quizzes
There are four weekly quizzes. You may begin submitting them as soon as the course opens.
Quiz 1 is due at the end of the first week, Quiz 2 is due at the end of the second week, Quiz 3 is
due at the end of the third week, and Quiz 4 is due at the end of the fourth week.
Quiz Scoring
You may attempt each quiz up to 3 times in 8 hours. The score from your most successful
attempt will count toward your grade.

Grading policy
You must receive a final grade of 70% or better on each assignment (quizzes and project) to pass
the course.

Your final grade will be calculated as follows:

• Quiz 1 = 10%
• Quiz 2 = 10%
• Quiz 3 = 10%
• Quiz 4 = 10%
• Exam 1 = 15%
• Exam 2 = 15%
• Exam 3 = 15%
• Exam 4 = 15%

Differences of opinion
Keep in mind that currently data analysis is as much art as it is science - so we may have a
difference of opinion - and that is ok! Please refrain from angry, sarcastic, or abusive comments
on the message boards. Our goal is to create a supportive community that helps the learning of
all students, from the most advanced to those who are just seeing this material for the first time.

Plagiarism
Johns Hopkins University defines plagiarism as "...taking for one's own use the words, ideas,
concepts or data of another without proper attribution. Plagiarism includes both direct use or
paraphrasing of the words, thoughts, or concepts of another without proper attribution." We take
plagiarism very seriously, as does Johns Hopkins University.

We recognize that many students may not have a clear understanding of what plagiarism is or
why it is wrong. Please see the following guide for more information on plagiarism:

http://www.jhsph.edu/academics/degree-programs/master-of-public-health/current-
students/JHSPH-ReferencingHandbook.pdf

It is critically important that you give people/sources credit when you use their words or ideas. If
you do not give proper credit -- particularly when quoting directly from a source -- you violate
the trust of your fellow students.
The Coursera Honor code includes an explicit statement about plagiarism:

I will register for only one account. My answers to homework, quizzes and exams will be my own
work (except for assignments that explicitly permit collaboration). I will not make solutions to
homework, quizzes or exams available to anyone else. This includes both solutions written by
me, as well as any official solutions provided by the course staff. I will not engage in any other
activities that will dishonestly improve my results or dishonestly improve/hurt the results of
others.

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