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.

rm command is very dangerous because after you remove something, you can not recover it. There is no trash bin in the unix system. If you have some raw data…

cores, cpus and threads :\ http://www.slac.stanford.edu/comp/unix/package/lsf/currdoc/lsfadmin/index.htm?limcore_detection.html~main Traditionally, the…

I am running pyclone recently to determine the clonality of our collected tumor samples. It needs tumor purity (estimated from sequenza) for input. I have…

you can copy to your home directory.\ it changed the key binding from control + b to control + a if you are familiar with the screen shortcuts.\ control + a…

I have a 26 G tsv file with several thousand columns. I want to extract 500 columns from it based on the column names in another file.

If you ever wants to use R on the command line, now you have several opitions.