Course is good, Exam 4 requires extra instructions. DO NOT USE ANNOTATIONS WITH TOPHAT!

Good course to improve your command line skills in analyzing genomic data.

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

A worthy introduction to the problems facing computational biologists.

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

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

I like the course too much,

this is a useful course

Excellent presentation

Very good course

Useful course.

I feel like this course started off well with an insightful introduction to UNIX, but then missed the chance to reach its full potential. While the introduction to SAM, BED, GTF, VCF etc. formats is very helpful, tools like bowtie2 and tophat are already outdated. Some important aspects were explained in only a few seconds, while quite some time was spent on correcting the commands (the usage of shortcut keys to navigate the command line might have been helpful). The lectures very therefore quite tedious.

If you are new to the topic, it might be pretty confusing and, personally, I was prone to mix up many of the tools, like samtools, bedtools, bcftools, that have very similar names and perform somewhat related operations. It would have been very helpful from a didactic point of view to provide a few overview slides that structure all the relevant tools and their commands and group them into application fields . This would make it easier for the learner to grasp their interrelationships.

All in all, a helpful, but not ideal, course for anyone who is interested to learn more about the practical aspects of analyzing and aligning NGS data to the genome.

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.

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

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.

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.

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.

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

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.

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.

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

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.

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.

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.

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.