Computational biology and genomics
I have been using pnas_expression.txt as a test dataset for count table analyses for many years. It was created by Davis McCarthy and was hosted on their Google Sites website. After some time, the site became unavailable and I have been hosting it on my web server since then. The RNA-seq libraries were generated using…
Recently I have been learning about Singularity and have been experimenting with building Singularity images. However it seems that there is no layering in Singularity, which exists with Docker and Dockerfiles. This is quite convenient to have because building will resume from the point where the last step failed. However the comment: You can build…
I just finished reading "Using prototyping to choose a bioinformatics workflow management system", which I summarised on Mastodon as follows: Enjoyed reading "Using prototyping to choose a #bioinformatics workflow management system". Paper describes authors’ 10 day experience searching and implementing a workflow. Summary: Need to decide which tool to use? Shortlist a list of potentially…
When I was first learning about SAMtools, I kept my notes in a Wiki. I would type the SAMtools commands in the terminal and copy and paste the output into my Wiki. It was a tedious task but it was a useful resource that I would refer back to frequently. The latest version of my…
Updated 2018 May 29th to include example using a config file As promised two years ago, here’s a short blog post on Snakemake. I have been using Bpipe to manage my workflows/pipelines but Snakemake has been mentioned to me on more than one occasion; in particular: @davetang31 seems useful if testing many diff types of…