This is one of the most discussed topics especially in Clinical Genomics! Affordability, accuracy, feasibility and of course time consumption - based on these factor mostly, which sequencing technology is more suitable for clinics? Whole Exome Sequencing or Whole Genome Sequencing? (WGS or WES, WGS vs WES) So here's my 2 cents on this discussion! When it comes to DNA sequencing there has always been a raging debate over the choice of Whole Genome Sequencing (WGS) or Whole Exome Sequencing (WXS) for routine use. Whole genome sequencing (WGS), as the name suggests is the process of obtaining the entire genome. In most cases however, this is far from practical and only 95-97% of the genome is covered because it is technically difficult to sequence certain regions of the genome (high GC content, large repeat regions, centromeres, telomeres, etc.) with existing technology. “It’s very fair to say the human genome was never fully sequenced,” - Craig Venter “The human genome ha
So, I tried installing Sleuth along with Kallisto for RNA-seq data analysis. Getting Kallisto to work was no big deal but Sleuth required a couple of dependencies even before installation. Following instructions on github and on other online tutorials which seemed pretty straightforward as in any R-Bioconductor based installation, I expected this to go smooth. Much to my surprise, it wasn't a cake walk! Sleuth requires us to install 'devtools' and 'rhdf5' from within biocLite in R (I think we could google a little about what these packages do). I had a fresh 64-bit BioLinux-8 installation which is basically a Linux Ubuntu 14.04 based OS, comes bundled with many preconfigured bioinformatics packages including a R version 3.2.0. Initially running biocLite('rhdf5') didn't throw any error and went all the way with just a couple of minor version warnings but biocLite('devtools') threw numerous errors and just wouldn't work. After a few