Thursday, June 30, 2016

Syntax Highlight Code in Keynote or Powerpoint

I came across this awesome gist explaining how to syntax highlight code in Keynote. The same trick works for Powerpoint. Mac only.
  1. Install homebrew if you don’t have it already and brew install highlight.
  2. highlight -O rtf myfile.ext | pbcopy to highlight code to a formatted text converter in RTF output format, and copy the result to the system clipboard.
  3. Paste into Keynote or Powerpoint.
If I’ve got some code in a file called eset_pca.R:
I can simply highlight -O rtf eset_pca.R | pbcopy and then paste it right into Keynote or Powerpoint.

Wednesday, June 1, 2016

Covcalc: Shiny App for Calculating Coverage Depth or Read Counts for Sequencing Experiments

How many reads do I need? What's my sequencing depth? These are common questions I get all the time. Calculating how much sequence data you need to hit a target depth of coverage, or the inverse, what's the coverage depth given a set amount of sequencing, are both easy to answer with some basic algebra. Given one or the other, plus the genome size and read length/configuration, you can calculate either. This was inspired by a similar calculator written by James Hadfield, and was an opportunity for me to create my first Shiny app.

Check out the app here:

And the source code on GitHub:

Give it your read length, whether you're using single- or paired-end sequencing, select a genome or enter your own. Then, select whether you want to calculate (a) the number of reads you need to hit a target depth of coverage, or (b) the coverage depth you'll hit given a set number of sequencing reads. Once you make the selection, use the slider to adjust either the desired coverage or number of reads sequenced, and the output text below is automatically updated.

Shiny App: Coverage / Read Count Calculator
Creative Commons License
Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License.