Command Line Tools for Genomic Data Science

Useful course.

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.

nice design

Great course. I think it should be the first in the whole series.

This was one of the most valuable courses I have taken online. Thank you

Clear, very practical and applicable

Could have more tools introduced, for instance SNP calling tools.

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.

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

Great resource to learn unix codes and prepare your self for analysing genomic data

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.

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.

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.

Very fine course. drills students well. would prefer if files used in examples were provided for students before the class. it makes life easier. would also prefer students are advised how to install tools on their laptops. Good course overall and I learnt much

Detailed and challenging.

A lot of things are not explained in the course

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!

Excellent Introduction to Command Line Tools used in High Throughput Sequencing Analysis.

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

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

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.

I like the course too much,

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.

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.