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

4.2
297 ratings
83 reviews

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

JJ

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.

GV

Mar 14, 2016

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

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51 - 75 of 81 Reviews for Command Line Tools for Genomic Data Science

By Andrew J D

Aug 27, 2018

Very informative course. Only downside is that the example datasets/scripts are not provided (which I tend to find to be useful for learning informatics).

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.

By Xing Y

Oct 02, 2018

The course is good but not "self-contained"...

By Geoffrey K

Apr 22, 2019

A worthy introduction to the problems facing computational biologists.

By Thiago C S

May 15, 2019

Some questions were way too specific and out of scope from real practice.

By Stefanie M

Feb 10, 2019

A lot of things are not explained in the course

By Anna B

Feb 08, 2019

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

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 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 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 shipra v g

Apr 09, 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 Onur S

Feb 20, 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 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 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 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 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 Noam H

Jun 02, 2019

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

By José A C E

Aug 04, 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 yingchuan q

Jul 22, 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 David h

Apr 14, 2016

If you want to know the array of options of the various tools in the Tuxedo suite (and don't want to read a manual), then this course is for you. I was hoping that there would be some conceptual grounding in what each tool was useful for, but that was not present at all.

By QIHUA Z

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 María E P R

Jul 02, 2017

It was a really hard course, I think the focus was not in to learn what specific command lines tools does otherwise was how to use a command line tool . Another problem that I have was that the most of videos don't have transcripts or subtitles, this make it harder than usual.

By Allan T S

Nov 13, 2016

The video lectures are confusing and quizzes too

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 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.