— Sam Nicholls (@samstudio8) October 7, 2015
The adventure continues, here’s what I’m working on lately.
Yesterday, I gave a talk at the Aberystwyth Bioinformatics Workshop on the metahaplome: a graph inspired structure for encoding the variation of single nucleotide polymorphisms (SNPs) observed across aligned sequenced reads.
I wanted a BAM that contained reads aligned to just one of the many contigs the file contained. As usual, I made this much more difficult than it really ought to have been.
This afternoon I wanted to quickly check whether some reads in a BAM would be filtered out by the GATK `MalformedReadFilter`. Turns out that GATK is pretty unforgiving if you forget that filter is automatically applied by `PrintReads`.
Recently I’ve been following the GATK DNASeq Best Practice Pipeline for my limpet sequence data. Here are some of the mistakes I made and how I made them go away.
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 […]
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 […]
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 […]
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 […]