Aaron Mitchell-Dick
Bioinformatics you can follow.
Step-by-step walkthroughs for genomics analysis on the command line, in R, and in Python — written for the person running the pipeline for the first time, and commented with the things an experienced analyst knows and forgets to say out loud. Every command is one you can paste and run.
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Who this is for
These walkthroughs assume you have sequencing data and a biological question, and that nobody has explained what conda activate does or how your transcript IDs will match your annotation. They are written to be run start to finish, in order, on your own laptop.
If you would rather not write code at all, Galaxy is an excellent free, open-source, web-based alternative for the entire bioinformatics community.
Ground rules
Every walkthrough on this site follows the same conventions, so that once you have read one you know how to read the rest.
| Convention | What it means |
|---|---|
| Code blocks are shown with the shell or language they belong to | bash blocks run in a terminal; r blocks run in the R console or RStudio |
| Output blocks appear directly under the command that produced them | These are real results from a real run, not invented examples |
| Paths are written as placeholders | path/to/your/data always means substitute your own path here |
| Versions are stated where they matter | Where a command is version-sensitive, the version is named in the text |