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hackyhour

Source for information on fortnightly bioinformatics help session

What went wrong? How to spot your mistakes and fix them

We have all been there: You have followed all the right steps, have triple-checked the commands, and somehow it doesn’t work; or, you think it works but then the results don’t make sense; or, nonsensical error messages seem to scream at you. Next Wednesday we will share some of our own mistakes, errors, FUs, boners, mishaps, catastrophes, and how we fixed them (at least sometimes). And we will try to explain how sometimes even the best designed pipelines don’t survive the first dataset.

Question of the week: Do you know what the words ‘snafu’ and ‘fubar’ mean, and where they originated?

Here are explanations for snafu and fubar if you are curious.

Why pencils have erasers

Here are a few links that list common mistakes in bioinformatics:

Common stupid mistakes in bioinformatics

More common mistakes in bioinformatics

How not to be a bioinformatician

The first step that most of us do is google the error message. Sometimes the trick is how to phrase the search. The following websites often come up when you google an error message, but here are the main pages.

Stackoverflow

SEQanswers

Biostars

Google Groups and GitHub

Two of the best places to keep up on what is going on with a particular program or software package are Google Groups and GitHub. Be sure to check if there is a google group for the software that is giving you problems. Feel free to post your questions; often the developer themself will post an answer and respond to questions. Just do a search on the site to make sure someone else hasn’t already had this issue. If the software is on GitHub, then you can check the Issues tab and browse or search there for a similar problem (sometimes googling misses these, depending on how you phrase the search).

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