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Exome or Whole Genome Sequencing?

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...
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Installing Sleuth for RNA-seq analysis

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 minutes of googling, I ended up upgrading the R-version to the latest using the steps here.

But biocLite('devtools') simply wouldn't want to run error-free. Whatever I try, installing individual dependencies manually or try to start R as super user, it simply wouldn't give in.

At one point, there was a warning that said too many errors, terminating installation.
The one big error that kicked off the cascade was

dpkg: error processing r-base-core (--configure): causing build error


I googled again with search terms like "devtools failed to process build dependencies" but without much luck.. and finally I found the answer on this stackoverflow thread.

Basically the best way to go about this was to get out of R on to normal terminal and then update the devtools through gnutls using the usual apt-get command.

Here are the commands to solve the devtools problem.

apt-get -y build-dep libcurl4-gnutls-dev
apt-get -y install libcurl4-gnutls-dev
Once this is done, I went back to R and ran the commands

biocLite('rhdf5')
biocLite('devtools')
biocLite('pachterlab/sleuth')

Worked like magic!! Now I have Sleuth running smoothly! yayy!


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Venkatesh Chellappa







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