Hi Bioinformatics lovers,

Welcome back to chatomics (my newsletter and YouTube channel name)!

If you are like me who is overwhelmed by the NEW data types generated by NEW technologies, and NEW tools coming out daily for analyzing the data? Today's newsletter is for you.

Take single-cell RNAseq for example, you probably see new bioinformatics tools out every week. Which one to use? This is my process...

If I do need the exact functions of a couple of similar packages, I will first go to their github page and see how good the documentation is. They should give you detailed instructions on how to install, what's the input and what's the output etc.
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ALSO, pay attention to how well they maintain the packages. Do any people answer questions for the github issues? Packages in Biconductor usually have better support. Go to https://support.bioconductor.org/ to ask questions.

If I do not need the tools now, but it may be helpful, I will curate it on my own github page. (NOTE, writing down is so important. Because you can not trust your memory). I can always go to my own github page and quickly search and find the tools later if I need them. MY SUPER POWER:)

I am jumping ahead of myself...

How do I even know which tools are out? Six tips:

1. Stay on social media. Register a Twitter/X account, follow labs/PIs doing bioinformatics, single-cell, tool development etc.
2. Join a community. You can join online communities, such as BioStars, Seqanswers, Reddit’s Bioinformatics community, and the Bioinformatics Stack Exchange.
3. Subscribe to journal news. For example, I subscribe to Genome Biology. Whenever there is a new paper published, I get notified.
4. read blogs! e.g., https://www.rna-seqblog.com/ including mine :) divingintogeneticsandgenomics.com​
5. Go to conferences. E.g., Intelligent Systems for Molecular Biology(ISMB), Bioconductor annual conference.
6. Lastly, read this post by Steven Turner https://gettinggeneticsdone.blogspot.com/2017/02/staying-current-in-bioinformatics-genomics-2017.html I read the 2012 version of this post when I started to learn bioinformatics.

If you want to watch the video, here it is.

Although Bioinformatics develops very fast, if you have a solid foundation of basic skills you do not need to worry.

Basic skills like:

> quick learning
> Strong Unix skills
> understanding biology.
> strong R/python programming skills
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You can always quickly learn (by doing) how to analyze a new data type.

For example, I am interested in long-read sequencing, but I have never done it myself. But with my basic skills, if I need to do an analysis in the future, with some tutorials and a real project, I am confident I can learn it in a couple of months.

That's it for today!

I do not want to JUST teach you how to write a program to analyze specific data types (that's important), but I also want to teach you how I think about bioinformatics and the more important skills that will not get outdated.

Happy Learning!

Tommy

PS:

If you want to learn Bioinformatics, there are four ways that I can help:

1. My free YouTube Chatomics channel, make sure you subscribe to it.
2. I have many resources collected on my github here.
3. I have been writing blog posts for over 10 years https://divingintogeneticsandgenomics.com/​
4. Lastly, I have a book called "From Cell Line to Command Line" to teach you bioinformatics.

Stay awesome!

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