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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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1 - 25 of 148 Reviews for Command Line Tools for Genomic Data Science


Jun 20, 2018

I have to be honest. This course was bad learning experience for me. Watching the videos was a waste of time. The instructor is just typing commands without properly explaining the context. All you learn from the videos is probably a list of names of the tools you can use and some of it's syntax, which really doesn't require hours of tedious videos. It may be more productive just to look at the name of the tool and go google by yourself. Watching the videos is like someone telling you HOW to use the tool (how to type the command), but didn't tell you WHAT the tool is doing, and WHY we want to use these tools. The HOW port is explained, but the WHAT and WHY parts? Sorry it's not there. What's funny is that, in the quiz they ask you WHATs and WHYs! At that time you would be thinking: "yea, these are good questions! but they were never explained in the videos. Would have been nice if these knowledges were covered!" That's the time when you go googling, hoping the get some answers to pass the quiz.

By Jaydeep S

Apr 30, 2018

This is a very poorly designed and executed course. The teacher should have used a bit more practical examples and the video lengths is too long. I have to leave it halfway, because I don't see any point of wasting my time with it. Its sad that this is part of such a great specialization module. I hope the user comments allow the course designers to implement some changes to this course.

By Jason M

Nov 30, 2017

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.

By Jia Q

May 31, 2021

It has been a struggle for me to take the course. I am in 2021, the virtual linux system the course provided is a bit out of date, it has taken me a lot of time to get it normally functioning.

(WARNING for incoming friends: if you can't get the centos6 system they provided working, I would recommend not to take the course, because nearly all the quiz projects require the tools that were already installed in that system. I've tried to install them on my own system, but it was extremely hard to have them all, and requires extra knowledge in linux.)

I can feel the lecturer knows a lot, but she is not explaining things clearly. We need to use a lot of tools for different purposes and the output data is quite hard to interpret, but during the lessons, most of the time was wasted on typing the codes, without explanation. Also the English subtitles are terrible, there are a lot of errors, quite unfriendly for non-native speakers.

But the good thing about this course is, it has covered the basic workflows for genome assembly and transcriptomics, at least it provides a guideline. But need a lot of extra work (even more than the lecture time) to google and read other instructions. The project quizzes are quite hard (not about the codings, it is still the problem of lacking explanation). After completing it, I took some time to summarize the whole workflow, and I found it quite helpful for understanding the whole process.

Overall, this course teaches super cool things, but in a poorly organized manner. I didn't find any other course on coursera that could substitute this course. So just bear with it if you really want to learn linux commands for genomics.

By Paul S

Aug 29, 2018

The instructor clearly knew her material. She tried to present it systematically with enough information to give students the ability to perform the programming tasks. There were, however, a number of areas where there is substantial room for improvement.

1. The slides were underutilized. Listing a command name is not enough information to use it. For the most part this was adequately done in the lectures, but having details on critical implementation formats in slides would have been a helpful visual.

2. The class was all about using command line instructions. When the command line was shown on screen it was hard to read and frequently covered over by the video controls. Moving it up and making it large enough to read would be very helpful.

3. Although some details of the output file structure were presented a lot was left for the student to dig out of other sources. If you don't know what to look for this makes things very difficult.

4. The class is about using genomic analysis programs but the instructor did not provide information about where to download the appropriate files from.


May 24, 2018

This class really needs to be redone. In fact, it would be more productive to work off of the tools with python and/or galaxy. This class is essentially watching someone type and then trying to figure everything out on your own afterwards. It is not productive to learning the material, and will not help any of the students. I thought that the galaxy class was bad, but considering it is 4-star compared to this one!!

Not only was teaching helpful tools not accomplished, but it required installation of the VM box which modified my registry! I will not have to uninstall everything and return my Windows to a previous start point to undo the issues it is causing. I am actually pretty angry that I had to take this class to get my certification. seriously, replace it with something helpful!! watching someone type (and tiny type at that) does not promote learning.

By Marc B

May 1, 2020

This was one of the worst courses I had on Coursera :( The content is more focused on learning command line arguments and how to use unix tools rather than on the rationale behind the tools and what the arguments are doing. Even worse, the content of the video lectures is often not sufficient to solve the quiz/exams. Either there is content that is neither mentioned nor referenced in the lecture or there is too much ambiguity in the instruction/question to deduct a clear answer.

The virtual machine image is not usable nowadays and with different versions of the tools you can't solve the exams. It was really a frustrating experience this course :(

By Damian D

Jun 2, 2020

This is a course of googling. The lectures give some idea the general pipelines in genomic analysis and show the usage of the most essential tools. However the Instructor sometimes uses commands that she does not explain and the data structure is completely elusive. The exams are badly designed and poorly explained. They take MUCH more time than expected. With a rudimental knowledge about the command line language I was able to finish the course but it was painful. I do give 3 stars cose I think I learned quite a bit during the course. As painful as it was at times. IMPORTANTLY, Instructor is absent from the forum and it seems she pretty much abandoned it.

By Amy G

Feb 16, 2019

This course is not at all up to the standards set by its companion courses. The assignments require a VMbox that is broken, the transcripts are way off base, the tools are somewhat out of date, and the content and message board reflect lack of sincere oversight and care for student experience. Yes, it is possible to pass if you are diligent. Yes, it contains useful commands. No, it is not at all worth the effort. It should be replaced, removed for the sequence, or severely revised.

By yingchuan q

Jul 21, 2018

It is not that the course is not useful; there is a LOT of room for the course to improve itself. One major issue is the lecture lacks sufficient descriptions why we do particular things, and the instructor's non-native English speaking and monotone worsen the situation such that I was often lost about the purpose of certain calculation. The second issue is that the course needs additional materials that aid students during the learning. The lecture video itself is not effective to provide sufficient guidance. I have done most of my learning by googling. In summary, the course was definitely poorly designed.

By Robert D

Jan 18, 2020

Overall, the content of this course is great. Much of the content I began using in my job (genomics biotechnology company) immediately - literally within 24 hours of learning. It accelerated my ability to accomplish tasks by a huge amount. I would give 5 stars just for the content, but I gave 3 because the exams are outdated and out of context. In Week 3, some of the content on the exam was not discussed in the course, and the last exam in Week 4 had many red herrings. You can figure out what you need to actually do by reading the Discussion Forum for Week 4, but the course material should be updated so that students don't waste their time on unneccessary activities.

By Jason

Jun 23, 2018

Thank you very much Dr./Professor, Liliana Florea. I've learned a lot. It's a very good opportunity to improve my knowledge. This means a lot to me.

By Gouri V

Mar 13, 2016

Very informative course. Because I am new to this, it was at times confusing. But overall, great teaching and great experience. Thank you.


Apr 18, 2021

The course is good overall. Many useful skills are introduced. However, the cufflinks package has been too old for transcriptome analysis nowadays, and some commands could be upgraded to the newest ones if possible.

By José A C E

Aug 4, 2019

I considered this course was condiserably harder than previous courses from the Genomic Data Science specialization due to lacking instructions and exams asking about concepts not reviewed in class, for instance, soft/hard links distinctions, the use of cuffcompare, a clear distinction between mate reads and paired reads, a thorough explanation of the use of CDS vs exon in gtf files. At the other hand, the difficulty possed by this course made it satisfying.

I would really like the course team and support to consider add complementary readings in order to help the understanding of topics not intensely reviewd in the videos.

By Anastasia R

Jul 21, 2020

There was no feedback in the forum. The last exam has misleading notes which is there from the beginning of the course (at least 4 years), but it seems that nobody cares to help students and to rephrase instructions. So, students have to help themselves. If you want to have the feedback about the course - check comments on the exam 4.

Exams require exact numbers which may slightly vary from version to version and from additional options which may be used (in the same way as it was shown during the lecture). Finally, it may take ages to people complete the exam even if the commands they use are correct. This does not help learning, however, consumes enormous amount of time.

By Yang Y

Aug 12, 2016

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 Ratatosk

Jul 4, 2021

This course is probably the worst course I have taken so far. There are no exercises to help you learn the code needed, just the lecturer reading the code. The code is shown on the screen, but is too small to read. There are endless boring lectures on file types but no real practice with them. If you arent running a unix machine (and even if you are) you will need to run a virtual linux box on your computer for this course, which is rather temperamental. The tools being taught are outdated. There is no help on the forums, the last post from a moderator, let alone staff, was several years ago.

By Makragić A

Feb 20, 2017

This is the worst course I've ever listened, and I've listened my fair share of online courses! Do this course ONLY if you want to complete whole specialization!

Professor is simply awful, English is not her native language obviously, but even that is not the problem, she simply speaks sentences that doesn't make sense at all! And she obviously doesn't have computer science background, if she does then she is even worse then I thought.

By M C

Dec 27, 2020

Terrible resources and planning! Several answers to quizzes/tests need to be changed and Coursera or JHU have neglected this course and not updated the errors. Several changes have been noted 4 or more years ago and still no updates. I have tried contacting Coursera and no one seems to care!

By Ash H

Nov 26, 2019

Very good course. Easy to follow and loads of useful skills and info.

It starts with some guidance on general Unix navigation and then teaches the format and tools for a range of different types of genomic data. Finally it teaches you to use tools for alignment and transcriptomics. It packs a lot in but plenty of demos and there's a chat board where you can ask questions.

I already had some experience with command line tools before doing this course but found I learned loads. If you don't have any experience with Unix or with bioinformatics tools I think you will find the course doable and you will learn a lot of very useful skills but it will take you a bit longer. I don't think you need to take the earlier courses to find this one useful. (I didn't.)

For me it was also useful to improve the organisation of my work when I'm doing data handling.

The online setup is good - it comes with pre set target dates for when to complete each module but you can reset them / push them back if needed. The videos have written transcripts underneath, these are mostly good but are made automatically so they occasionally mis hear more technical vocabulary. You can take the tests as many times as you want but only 3x every 8 hours.

By minli x

Jan 25, 2016

The course content is very solid. It focuses heavily on the tools and technique, and there lacks the concepts and biology behind those tools. But I would guess there is some prior courses in this specialization explaining the concepts, though I didn't take them.

The tools explained in this course is the most popular ones for handling up-stream analysis. They are the must-have ones for current bioinformatician jobs.

The instructor, Dr Liliana Florea, did a great job, walking you through those tools step-by-step. I also found the exercises (exams) highly useful.

The course title is not the most accurate one. The title is not very catchy either. This course is more about the tools for analyzing next generation sequence data.

By Tran N

Feb 25, 2019

It was a quite challenging experience, especially the final module. The problem you have to deal with is not "how to properly use the programs/tools", instead, we have to learn "how to play with the parameters" so that we can have the right answers for the quiz/exam questions. There were a lot of failures throughout this course, I had to watch the lectures again and again, deeply dive into the discussions in course forum, search google and seqsanswer/biostar forum, etc.... I became hating the lecturer and the mentors for theirs not so well organized lectures and answers ... But afterall, I've learned a lot. Thank you!

By Lilya N B

May 15, 2020

Key points: It is accessible to beginners and the teaching quality is good.

Taking this course was a pure enjoyment. I have learned so much about the use of command line tools in Genomics. Why they are used, how they are used and what are the most popular tools. This course offers a real good overview of the field in general.

The tools of the last week are outdated by now but for me, the whole take-away of that week was learning about the workflow of an RNA-seq analysis and its importance.

Highly recommanded course.

By Lindsay C

Feb 11, 2021

The material was very clearly, thoroughly, and patiently explained by Dr. Florea. I also appreciate how explanations on how to arrive at the correct answers for the quizzes were provided in order to facilitate better learning through hands-on experience. I am very grateful to Dr. Florea and everyone involved in this MOOC. A job very well done! Thank you.