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Learner Reviews & Feedback for Command Line Tools for Genomic Data Science by Johns Hopkins University

523 ratings

About the Course

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....

Top reviews


Nov 27, 2022

I use for decade UNIX command but this course opens my mind into new horizon on UNIX command , data science and I realize learn a lot from this learning time...

Big Thanks


Aug 5, 2020

There were some typos and confusion about the need not to follow the example code for Exam 4.

However, I thought that the course was good and useful overall.

Thank You!

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101 - 125 of 148 Reviews for Command Line Tools for Genomic Data Science

By Catherine J

May 19, 2020

Excellent presentation

By mora k

Jan 17, 2023

Very good course

By wenting w

Sep 10, 2017

Useful course.

By Kasper T K

Nov 21, 2017

Great course, the instructor does a great job in introducing the students to some off the important sequencing analysis tools. Some of the lectures are although a bit bland, where the instructor reads the entire contents of a slide for format files or program options, this is sometimes quite useless as you can read that yourself by... simply reading the slides.

Forums were not always very useful, sometimes solving error messages were supported by referring to the manual page, instead of actually bothering to look through the code for providing more constructive feedback on what goes wrong in a given example.

Instead, examples should be given which elaborates on the effects on chosen different parameters - like "If you want to make a local alignment, use the bla.bla option. However, beware that when using this, more errors are prone to be assigned...bla.bla.".

For the format, interesting columns in the format files in general are interesting, when looking for e.g. "amount of unique genes" etc.

By doing this, we would be helped better into understanding questions of the quizzes, while also delivering an even deeper understanding of the formats and tools.

By Onur S

Feb 19, 2018

I really struggled to complete this course. The extent of coverage of the topics is quite good, however this is a applied course and application part is lacking A LOT. The biggest drawback here is that the instructors demonstrations are not accessible to learners. This limits the learning experience so much that you get stuck even at the easiest question in a module exam. Some questions in the exams really require the learner to think and do google searches to figure out a strategy to answer the question (this is a good thing, though). However, it can be very easy to get bogged down and lose focus while figuring out what's going wrong. It is advised to visit discussion forums before taking module exams. I think you should not expect to master the presented tools after finishing the course, but you will still get a decent understanding of them

By Emil C F

Feb 3, 2020

Great inclusion in the specialization. I never knew anything about shell until now and I feel like I can use a lot of things from the course in my day-to-day data treatment/processing tasks. I am only giving 3 stars because I spend about 40-50% of the time troubleshooting technical things. The CentOS Vmbox is a great idea but that hardly worked for me (it interfaced weird with OSX and I could get it to understand my keyboard layout, shared folders did not work either) and was a source of frustration. One suggestion for the course would be to help the student verify the initial data set before completing all the analyses on it ... e.g. in the reading section mention the length of the output or similar. Twice I filled out an entire exam "correctly" but had the wrong initial output. You don't learn a lot from that but it does take a long time.

By Mafe C G

Aug 17, 2022

It's a good course, however the classes are not well structured and the what the instructor explains, is in many (most of the) ocassions, very confusing! Unfortunately the instructor doesn't speak clearly and the english subtitles can be extremely misleading.

What I really missed were the toy files to play with at the same time the instructor gives the lecture. They were NOT included in the materials of the course.

I really like Coursera and in my experience the couses are of outstanding quality, both the videos and the course material. Sadly this course simply doesn't meet the standards I was used to having with Coursera.

By Manuela L

May 7, 2021

This course is a good introduction to using command line if you're a complete beginner. However, this course needs a total update (this is the most outdated course I have taken in the specialization so far). Most of the tools used are already deprecated (TopHat, Cufflinks) but you still need them to pass the exams. Finally, there is no interaction in the forum and no answer to the messages, so you will have zero help from the staff. If you need to earn a course certificate, do not take the course. I am still surprised coursera charges for this course.

By Mark

Apr 10, 2022

Needs to be updated to use the latest versions of the tools. In 2022, many of the tools used in this course are now aging and some are end of life and, therefore, it would be nice to learn the techniques using current tooling. For example, tophat2 has now been superseded by HISAT2.

The videos are ok and contain a huge amount of useful information but some of the other courses in this specialisation are more engaging.

By Igor L

Jul 11, 2018

Very interesting material, but presented in a very dry manner and without going into too much detail. You do have to have some background in Linux and Biochemistry of DNA and RNA, otherwise it could be very hard to understand. Also, the last test deviates somewhat from what is presented in Week 4 lecture. Be very careful and read the questions with alertness before answering them

By Artur K

Jun 3, 2022

This is a rather weak course. It consists mostly of videos watching the instructor type (and mis-type). There is far too little attention given to exposing the underlying ideas, nomenclature used by the tools, connections - i.e. the big picture understanding is missing. In order to pass the exams, you'll have to search for and learn the information from other sources.

By Raymond F

Aug 14, 2017

Presentation was less lively than the others. Exercises prone to errors unrelated to the course objectives. A lot hof hints based on questions that are repeated a lot on the forum should be incorporated or stressed more in the exam instructions.

By Tom S

Oct 14, 2018

The theoretical lectures are ok, but the practical ones are a bit slow. Could have been more scirpt based from the beginning. The Exams are quite different from what is explained in the lectures I think. Especially in week4.

By Pedro S S

Jan 22, 2021

I didn't find funny the way to explain the lessons, although the organization of the material was cool. Maybe, a little outdated for 2021, but I know the course is 6 years old. In conclusion, good for knowing the basics

By Shipra G

Apr 8, 2017

I would prefer the lecture command line notes too in presentations or any other files in each week modules. It was difficult for me to understand her way of teaching and I felt the lectures didn't flow correctly.

By Rafael O B

Sep 22, 2021

Gives the basics for genomic analysis but the RNA-seq part is outdated. The tools used in the course such as cufflinks or Tophat are deprecated. There are other more recent tools that should be used instead.

By Ian P

Jul 12, 2018

I would have liked a better overview of the analysis process, less on details of command line parameters. there were several errors in the slides. The assignments were tedious and not very instructive.

By Sofia M K

Oct 18, 2018

Some of the tools are not up to date (tophat) and some things were unexplained. The focus was only typing the commands but not understanding why exactly we have to do specific things.

By Avishai B

Dec 19, 2016

It gives a significant coverage of many important command line tools. Teaching level is not good, very difficult to follow.

By Noam H

Jun 2, 2019

Great and practical material. Instructions for tests aren't clear and sometimes very time consuming to understand

By 朱永載

Feb 24, 2022

There can be more practice between the lectures instead of having all the practicals in the exam.

By Rigel Q L

Jan 6, 2022

The transcriptions are unccurate and needs to upgrade.

By Anna B

Feb 8, 2019

Exams take way longer than suggested, rest is good-OK

By Boyu J

Jan 18, 2022

Quizes in this course needs to be further orgnized.

By Dongyuan W

May 15, 2020