Github repository for R scripts
https://github.com/IamIamI/
R
Plasmid copy from coverage
Additionally to analyzing quality of samples, you can also use coverage to predict copy number of extrachromosomal elements. If chromosomal templates and extrachromosomal templates are in a 1:1 relationship, you expect equal distribution of coverage.
Sequencing read analysis
Ever wondered how to assess the quality of your NGS data? But get confused about all the fancy tools? Well how about i told you you can assess a lot of problems before even looking at the mapping yet, just by extracting some basic coverage data from BAM files, and extracting the number of reads per sample.
Roary analysis
Roary is a great bioinformatics tool, but it’s output is lacking some shine. Let’s try to polish it up a bit!
Plotting Geo data
This was a fun one. We had samples from different regions in two countries. Instead of showing a table, i wanted to show a summary per province on a map.
Multi Y-axis plots
This one was a confusing one. Putting three different datasets, containing values in different ranges, into one plot. Let’s get started!