Unix

To not miss a post like this, sign up for my newsletter to learn computational biology and bioinformatics. In my last blog post, I talked about some common bioinformatics mistakes. Today, we are going to talk about THE MOST common bioinformatics mistake people make. And I think it deserves a separate post about it. Even some experienced programmers get it wrong and the mistake prevails in many bioinformatics software: The one-off mistake!

To not miss a post like this, sign up for my newsletter to learn computational biology and bioinformatics. This post is inspired by this popular thread in https://www.biostars.org/. Common mistakes in general Off-by-One Errors: Mistakes occur when switching between different indexing systems. For example, BED files are 0-based while GFF/GTF files are 1-based, leading to potential misinterpretations of genomic coordinates. This is one of the most common mistakes!

To not miss a post like this, sign up for my newsletter to learn computational biology and bioinformatics. The other day, I saw this tweet: Machine learning and bioinformatics tutorials these days pic.twitter.com/0FhWWG09TB — Ramon Massoni Badosa (@rmassonix) May 15, 2024 Many of the bioinformatics tutorials are like that. I am not saying the tutorial is not good. For beginners, we need something basic first to understand it.

I need a transcript to gene mapping file for Salmon. I am aware of annotation bioconductor packages that can do this job. However, I was working on a species which does not have the annotation in a package format (I am going to use Drosphila as an example for this blog post). I had to go and got the gtf file and made such a file from scratch. Please read the specifications of those two file formats.