Computational biology and genomics
I highly recommend using RStudio if you use R because it makes working with R so much easier. I primarily use RStudio for writing up my analyses in R Markdown. Some RStudio features I couldn’t live without include: Vim keybindings, code completion, and code highlighting (rainbow parentheses are awesome!). Other nice features I like to…
The GROUP BY statement allows you to perform operations in a group wise manner. I first learned of the Useful FILe and stream Operations (filo) repository a long long time ago and keep coming back to it over and over again. The filo toolkit comes with three tools: groupBy, stats, and shuffle. The groupBy tool…
I recently came across this question: “You have a function called random that randomly generates a number between 0 to 1. Use this to calculate pi.” Worded differently, the question is asking you to estimate pi using random numbers. As you can read in the script for Life of Pi (one of my favourite movies):…
As of today, it has been a decade since my first post on this blog. It started aimlessly during my PhD as a place to post analysis notes for myself and ten years later it still remains so. However, over the years I have started to focus more on better project management practices and on…
This post is a continuation of a series of posts on the sequence analysis of SARS-CoV-2; see part 1 and part 2 if you haven’t already. Since my first post, I found out that you can blast sequences against a Betacoronavirus database on NCBI BLAST. The database, as of 2020/03/10, has a total of 7,844…
I ended my previous post on the sequence analysis of SARS-CoV-2 with the amino acid alignment of the spike protein from SARS-CoV-2 (MN908947) and Bat coronavirus RaTG13 (MN996532). The spike protein is of specific interest as it is due to its binding with the angiotensin converting enzyme 2 (ACE2) receptor that it is able to…
The article “A new coronavirus associated with human respiratory disease in China” released the full genome sequence (29,903 nt) of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the paper, meta-transcriptomic sequencing was performed on bronchoalveolar lavage fluid (BALF) from a 41 year old male suffering from a severe respiratory disease. Contigs were assembled using…
Some of you may have noticed the Buy me a coffee link I have on my blog. I have just used all the contributions to help pay for the hosting fees; this blog should be here for another two years (extended up until 2022 April 24). Thank you to everyone who has bought me a…
If you are planning on running some of the GATK workflows locally you will require various reference files, known as the Resource Bundle. Initially I had downloaded the files using FTP but I later realised various files were missing from the FTP server, such as BWA index and scatter files. Only later did I realise…
An approach I like to use when learning a new tool is to get started by trying to run an example and then gradually work out the details. In this post, I’m trying to learn the basics of the Workflow Description Language (WDL) so that I can adapt GATK workflows for my own use. WDL,…