Command Line Tools for Genomic Data Science

With genomics sparks a revolution in medical discoveries, it becomes imperative to be able to better understand the genome, and be able to leverage the data and information from genomic datasets. Genomic Data Science is the field that applies statistics and data science to the genome.This Specialization covers the concepts and tools to understand, analyze, and interpret data from next generation sequencing experiments. It teaches the most common tools used in genomic data science including how to use the command line, along with a variety of software implementation tools like Python, R, Biocon

( 82 Reviews )

Created by: Liliana Florea

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Overall Score : 76 / 100

Course Description

Introduces to the commands that you need to manage and analyze directories, files, and large sets of genomic data. This is the fourth course in the Genomic Big Data Science Specialization from Johns Hopkins University.

Time: 26h

Instructor Details

Liliana Florea

3.8 Rating
82 Reviews

Dr. Liliana Florea is an Assistant Professor of Medicine in the McKusick-Nathans Institute of Genetic Medicine, where she develops computational methods for analyzing large scale sequencing data to help characterize molecular mechanisms of diseases. Her research interests include comparing and analyzing genomes, characterizing genes and alternative splicing variations, and predicting non-coding RNA elements in human-virus interactions. Before joining the Johns Hopkins faculty in 2011, Dr. Florea served on the faculty at the George Washington University. Previously, she was a member of the team of scientists at Celera Genomics that produced the first sequence of the human genome. Her work has been recognized with a Sloan Research Fellowship in Computational and Evolutionary Molecular logy, and she received several early career awards while at the George Washington University. Dr. Florea holds a PhD degree from the Pennsylvania State University.

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By Ekaterina S on 5-Jan-17

Thanks for the great course. IT was just right level of easiness/hardness. While the quizzes were basic, the homework quizzes were hard but not unsolvable. These actually motivated to further spend time on familiarizing with the tools, whch is essential for home usage.Sometimes the videos had their length when we watched somebody else typing... that could have made better.

By Hathairat W on 6-Nov-17

Excellent quizzes and exams. Smooth flow of lectures. However, as a beginner I faced a lot of difficulty in installing the required tools. I could complete the course only because the tools were provided as a package with the VM box. I will be handling NGS data for my PhD project, for which I will have to install the latest versions of these tools. Manuals are cryptic. A lot of errors keep cropping up whenever I try to install anything. This course should have taught us that part too. I shall be thankful if you could provide a short course or a step by step write up for the same, else we will not be able to apply what such a good course taught us.

By Javier A D on 15-Apr-19

I really like this course! (The exams are a bit challenging though.)

By Nirav D on 9-Apr-18

A really hard introduction to bioinformatics pipelines, it was difficult but was stimulant!

By Benjamin S on 11-May-17

Great course. The last exam is a little bit tricky, specially when some commands are large and confusing. But with the help of forums, you can still find the right answers.

By Abdelbarre C on 9-Aug-16

Very detailed and simply explained introduction to work in linux environment for biologist

By Andria H on 11-Mar-16

Very interesting and detailed course.Most I liked the tasks: they are very detaild. Thanks to them I've leraned a lot of new things.

By Alexandre N on 17-Dec-16

I have learnt so much from this course.

By Sergio R on 23-May-17

Simple, straight forward and descriptive

By Silpa S on 11-Feb-16

Very bad or non-existent support

By Yang Y on 12-Aug-16

The worst course I've ever take in Coursera. I can pass the course all because I have some background of this topic. The lecture taught me NOTHING! Consider I just finish the previous course "algorithm for DNA sequencing" which might be the best course I toke in the Coursera, this course makes me very disappointed! If the previous course gives me the faith to continue learning something in Coursera, this course must be the reason that let me leave the Coursera left.I can't even understand why there are some guys give this course 5 stars. If there is -5 stars option, I'll put this score in front of the lecturer and tell her WHAT A BAD COURSE her give us.

By Jason M on 30-Nov-17

The worst class I've ever encountered in my life. The teacher mumbles to herself and the transcript often even says '[teacher mumbles]' at the critical point of the lecture. The majority of the class teaches useless and outdated material. Moreover, the quizzes reflect useless documentation details, as opposed to relevant content in genomics. To even do the quizzes, you're required to torrent their virtual machine image with an insecure checksum, thus compromising the security of your computer. The teacher herself clearly didn't read the documentation for the most basic Linux commands, hence she constantly uses inefficient commands, such as 'more' instead of 'less'. Altogether, this class is pathetic and will probably make you less competent in having wasted your time. Truly shameful.