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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