Hello Bioinformatics lovers,

It was Halloween! My kids dressed up as Hermione(from Harry Potter), creeper (from Minecraft), and a little red hat.

The kids had fun. Even my 2-year-old little red hat is not scared of those skulls and ghost decorations.

What is the scariest thing about Bioinformatics?

It is finishing that bioinformatics paper after you leave the academic institution.

Publishing can take A LONG TIME. I still have a paper dated back to 2018 from MD Anderson under revision.. but why is it scary?

It is so hard to REPRODUCE the figures after you leave. Luckily, for me, it is a different story.

I always write detailed documentation for my analysis and organize my project so that I can easily re-run the same analysis.

Take a look at how I documented my analysis to generate an enhancer-promoter interaction file from a public dataset https://gitlab.com/tangming2005/Enhancer_promoter_interaction_data/blob/master/bedpe/README.md

It was done 6 years ago, but I can still understand and use that file today.

Your future self will thank you if you make extra effort to write down the process today

In addition to documentation,

• For project organization, watch this video by me.
• For reproducible computing, read this paper and this paper.

I am a big advocate for reproducible computing. It is hard, but it is rewarding to get into the habit and learn how to make your analysis reproducible as much as possible.

And, one day, you will not feel scared at all and only have fun doing the analysis just like the kids enjoying Halloween :)

Happy Learning!

Tommy aka., crazyhottommy

PS:

I made a video on how to convert the bed file and bigwig file from hg19 to hg38 using crossmap. check it out!

Another one to explain Linux operating systems for bioinformatics here.

PPS:

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!