Posts Tagged ‘quality control’

The Tolls of Bridge Building: Part IV, Mysterious Malformations

   Sam Nicholls    3 Comments    Sanger-QC

Following a short hiatus on the sample un-improvement job which may or may not have been halted by vr-pipe inadvertently knocking over a storage node at the Sanger Institute, our 837 non-33 jobs burst back in to life only to fall at the final hurdle of the first pipeline of the vr-pipe workflow. Despite my […]


The Tolls of Bridge Building: Part III, Sample (Un)Improvement

   Sam Nicholls    One Comment    Sanger-QC

Previously, on Samposium: I finally had the 870 lanelets required for the sample improvement process. But in this post, I explain how my deep-seated paranoia in the quality of my data just wasn’t enough to prevent what happened next. I submitted my 870 bridged BAMs to vr-pipe, happy to essentially be rid of having to […]


The Tolls of Bridge Building: Part II, Construction

   Sam Nicholls    One Comment    Sanger-QC

Last time on Samposium, I gave a more detailed look at the project I’m working on and an overview of what has been done so far. We have 870 lanelets to pre-process and improve into samples. In this post, I explain how the project has turned into a dangerous construction site. While trying to anticipate […]


The Tolls of Bridge Building: Part I, Background

   Sam Nicholls    No Comments yet    Sanger-QC

I’m at the Sanger Institute for just another two weeks before the next stop of my Summer Research Tour and it’s about time I checked in. For those of you who still thought I was in Aberystwyth working on my tan1 I suggest you catch up with my previous post. The flagship part of my […]


Sanger Sequel

   Sam Nicholls    No Comments yet    Sanger-QC

In a change to scheduled programming, days after touching down from my holiday (which needs a post of its own) I moved1 to spend the next few weeks back at the Wellcome Trust Sanger Institute in Cambridgeshire. I interned here previously in 2012 and it’s still like working at a science-orientated Google thanks to the […]


The Story so Far: Part I, A Toy Dataset

   Sam Nicholls    No Comments yet    AU-PhD

In this somewhat long and long overdue post; I’ll attempt to explain the work done so far and an overview of the many issues encountered along the way and an insight in to why doing science is much harder than it ought to be. This post got a little longer than anticipated, so I’ve sharded […]