The guide I wish I had 12 years ago: a step-by-step guide to replicate a genomics paper figure

Two tools for plotting genomics data: figeno: Tool for making genomics figures in #python. https://t.co/Pe9dRxCCZO Plotting Multi-omic Data with plotgardener in #rstats https://t.co/SEp3wHAPzO

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10/ Takeaway: Chasing every tool is a losing game. Build the foundation that makes you adaptable—and unstoppable.

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9/ With those skills, you can pick up any *Seq method when needed. New protocol? No problem—you know how to learn it.

8/ Core skills that transfer everywhere: • Unix command line • R/Python • Visualization & EDA • Statistics • Reproducible pipelines

7/ Here’s the secret: You don’t need to master every pipeline. You need to master the foundations.

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6/ Tools age fast. Today’s “hot” Nature Methods tool might be unmaintained next year. Workflows evolve—your skills must too.

5/ Every method needs its own pipeline. Different QC, formats, aligners, and stats models. No “one-size-fits-all” workflow exists.

4/ Some probe single cells (scRNA-seq), some measure methylation, some map 3D genome structure (Hi-C). The list keeps growing.

3/ Each is a different beast. RNA-seq counts mRNA reads. ChIP-seq maps protein-DNA binding. ATAC-seq spots open chromatin.

2/ There are dozens of *Seq methods. RNA-seq, ChIP-seq, ATAC-seq… maybe over 100 if you count niche ones. New ones appear every year. see https://t.co/NTkz3G5JV8 (not updated for a while)

1/ I stopped trying to keep up with every new *Seq method— and my career got better. Here’s why that mindset shift matters.

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Last year, I visited EMBL in Germany. Kasit came up to me in the cafeteria and we took this picture. He then went back to Thailand, Bangkok after his postdoc. and then met one of the students (Krittiyabhorn) I taught online.

Check out Gene Signal Pattern Analysis--a new way of characterizing cellular state space (alternative to differential expression) lead by Aarthi Venkat, with @Joshilabyale! Today @LogConference! Also published in Nature Computational Science https://t.co/LksM5Ifi0z!

CellSAM A foundation model for Cell Segmentation Segment Anything Model - Vision Transformer https://t.co/xh1KvWQxSb Outperforming CellPose Similar to Human Applicable to Single-cell spatial transcriptomics Live-cell tracking 3D cell segmentation @davidvanvalen @naturemethods

the same day, another student wrote to thank me because he followed my tutorial 10 years ago! I am glad I made an impact on someone else's life. #bioinformatics #education

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Last year, I visited EMBL in Germany. Kasit came up to me in the cafeteria and we took this picture. He then went back to Thailand, Bangkok after his postdoc. and then met one of the students (Krittiyabhorn) I taught online.

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We spend months, sometimes years, building credibility with colleagues, clients, teams. But we can lose it all with one thoughtless action.

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