Storing FASTQ as unaligned CRAM

I was updating my BAM to CRAM post spurred on by a recent comment and then I wondered whether I could store my FASTQ files as unaligned CRAM files to save space. I thought it wouldn’t be possible because the reads are unaligned and therefore we can’t make use of a reference to save space…

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Updating my Docker documentation

In my last post I outlined an approach for automatically creating reproducible documentation using GitHub Actions. I have now updated my Docker documentation using the same approach but without using a container because then I’d have to run Docker inside a Docker container (which is actually possible using GitLab’s CI/CD platform but I haven’t tried…

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Creating reproducible documentation part 2

I had previously written about my workflow for creating reproducible documentation for SAMtools. The main idea was to generate the documentation via a R Markdown document that includes the documentation and the SAMtools commands to be executed on the command line (I do not know of another tool that can achieve this but if you…

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Grepping a list with a list

The grep command-line utility is a commonly used tool for searching plain text files for lines that match a pattern. For example, you could search a gene or SNP ID in a BED/GFF/GTF file to find out its coordinates. In this post, I will demonstrate how you can search for a list of things in…

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On blogging

When I was an honours student (in Australia an honours degree is a one year [in practice, it’s about ten months] undergraduate research program you can take after your Bachelor’s and has nothing to do with the traditional meaning of the word “honours”), I literally jumped into the deep end of bioinformatics. I recall joining…

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On learning

Sometime in the past this blog was called “Musings from a PhD candidate”, despite hardly writing any blog posts that were of the contemplative sort. It later evolved to “Musings from an unlikely candidate” because I had received my PhD, which I thought was quite an unlikely event given my background. However, this carried a…

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Add Docker to your toolkit

Docker has been around for 8 years and it has become a very popular platform for developing software. In the 2020 Stack Overflow Developer Survey, 39.2% of professional developers (total of 44,705) reported that they have done development work using Docker. Docker is only behind Linux and Windows! For the full list check out Stack…

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Creating reproducible documentation

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…

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Running RStudio Server with Docker

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…

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SQL group by statement on the command line

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…

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