Introduction to bash for data analysis 

Thanks for your comment. I was keeping it simple to demonstrate piping for beginners and decided to show it this way since they are equivalent in nearly all cases.

If you are working with large files on your institution's cluster or the cloud, or running NGS analyses, then you will mostly be working on the command-line. Windows machines have their command-lines in DOS, which won't run the bioinformatics pipelines that were all written for Linux/Unix. That means that most bioinformatics pipelines will run on a Mac just as well as on a Linux server, but they won't run natively on Windows, so you can run those tools on your institution's cluster or on the cloud instead, which you would probably be doing most of the time anyway. Mac users just have the added bonus of being able to feel like a hacker on their own computers, jumping around the file system and manipulating files like they do on the big servers. I typically don't run pipelines on my Mac (because they use huge files, many cores, etc.), but I do a lot of little things, including stuff like the mini-analyses I showed in the video.

Place this line between the colors: local NONE = "\ [\ 033 [0m \]" # Default Replace the line with this: $ " For this: $ ${NONE} "

Thank you mate!

Is your computer running zsh by any chance? If so, check this out instead: omgenomics.com/adapting-to-zsh/

@@OMGenomics Thank you very much! It's working now. P.S. I've replied twice to thank you and every time i write a reply, it gets deleted for some reason :D

Edit with vim or your favorite text editor instead.

Okay nevermind, new versions of Windows 10 64bit support a "Bash on Ubuntu on Windows", which emulates a bash in the cmd (at least this is what it looks like for noobs like me). "open" does not work, as it obviously can't find the default applications of Ubuntu, but vim or nano also do the job. Thanks a lot for this, it is quite hard to find good tutorials for total beginners!

Glad you found a way! For others who see this: To use bash you do need somewhere with a Mac or Linux OS to enter the code, which can often be in an institution's cluster where you have data stored and are running software from anyway. If any of you want to practice and don't have a computer system at your institution to ssh into (or a Mac/Linux computer), you can always use a virtual machine and install a Linux OS on it, and practice in there: www.virtualbox.org/wiki/Downloads

Yes it may only work on Mac. Try using vim or vi instead (may need to google some instructions for these), and also check if the ~/.bashrc file is called something else on your operating system. You can also skip those first steps if they don’t work, since they’re not required to follow the rest of the video, just helpful in general.

@@OMGenomics thanks for your quick reply, i will look into it and come back to you.

Haha, you know it’s funny how nobody caught that was a joke... trying to make the field more welcoming and less perfectionist about the little things. Oh well.

OMGenomics haha yeah I figured you were just messing around. I was just busting your chops ;) Also clarifying Incase someone didn’t know. Great content, thanks :)

@@OMGenomics great video. But all u have done on the data of pokemon can easily be done with excel with ease. Any thought?

i also now have had my bash cursor shifted once to the right after using this code... any ideas why?

also thanks for your vids, they're awesome!

hm it took some tinkering with the code but no more space before my cursor anymore... don't know exactly what it was but it is all in order now

Is your computer running zsh by any chance? If so, check this out instead: omgenomics.com/adapting-to-zsh/

@@OMGenomics Yes, now it works perfectly. thank you so much.