List of posts
- On stuck records and indel errors; or “stop publishing bad genomes”
- How accurate is the nanopore-only assembly of GM12878?
- With great power comes great responsibility
- A simple test for uncorrected insertions and deletions (indels) in bacterial genomes
- Let’s keep saying it, and say it louder: REVIEWERS ARE UNPAID
- It’s a bit POINTLESS if you forget the POINTLESS in POINTLESS ADMIN
- Judge rules in favour of Oxford Nanopore in patent dispute with PacBio
- Beautiful boxplots in base R
- HiSeq move over, here comes Nova! A first look at Illumina NovaSeq
- University of California makes legal move against Roger Chen (and Genia)
- Is the long read sequencing war already over?
- People are wrong about sequencing costs on the internet again
- Reading data from google sheets into R
- From there to here
- Tips for PhD students and early-career researchers
- Creating an image of a matrix in R using image()
- How to produce an animated gif of rise in global temperature in R
- Plotting cool graphs in R
- The unbearable madness of microbiome
- Why you probably shouldn’t be happy at Stern’s recommendations for REF
- Not providing feedback on rejected research proposals is a betrayal of PIs, especially early career researchers
- I can’t recreate a graph from Ioannidis et al – can you?
- Which reference manager do you use?
- Plot your own EU referendum poll results
- Open analysis of ZiBRA project MinION data
- Converting from GenBank format to FASTA using Microsoft Excel
- You don’t need to work 80 hours a week in academia…. but you do need to succeed
- Your strongly correlated data is probably nonsense
- Building a Kraken database with new FTP structure and no GI numbers
- We need to stop making this simple f*cking mistake
- Fast parallel access to data within MinION FAST5 files
- Shots fired – nanopore wars part II
- On preprints, open access and generational change
- Did you notice the paradigm shift in DNA sequencing last week?
- Doing the maths on PromethION throughput
- Bioinformatics error responsible for retraction in Science
- Dear NEJM…
- The age of the dinosaurs is almost over; NEJM publishes one of their last dying roars
- Which sequencer should you buy?
- Travel tips for highly organised and important people
- Online behavior, and an apology
- Generate a single contig, hybrid assembly of E coli using MiSeq and MinION data
- How to extract FASTQ from the new MinION FAST5 format using poRe
- The five habits of bad bioinformaticians
- We definitely do not need a “Steve Jobs” in biology
- What I know about the expansion of HiSeq X to non-human genomes
- What does the PacBio Sequel mean for the future of sequencing?
- Extracting MinION fastq on the command line using poRe
- Finally, a definition for bioinformatics
- Why nanopore sequencing errors aren’t actually errors
- Why I’m not jumping on the ORCID bandwagon
- Assembling B fragilis from MinION and Illumina data
- 4 predictions about nanopore sequencing in the next 12 months
- Why FPKM makes sense
- 101 bioinformatics facts
- Complete Genomics Revolocity and the future of genome sequencing
- Analysing MinION data with no bioinformatics expertise nor infrastructure
- How journals could “add value”
- On bioinformatics, and torturing the mechanic metaphor
- Excited by bacterial DNA in sweet potatoes? Check this out!
- On publishing software
- Recreating a famous visualisation
- You probably don’t understand heatmaps
- The cost of sequencing is still going down
- Defunding research excellence in Scotland
- How to not sack your professors
- How to recruit a good bioinformatician
- Putting the HiSeq 4000 in context
- Edinburgh and Glasgow invest in revolutionary HiSeq X clinical genomics technology
- Easy and powerful graph editing using R and PowerPoint
- 2014 in review
- Ripping apart that terrible Atlantic piece on Open Access
- A guide for running large projects
- On Mars, Venus, Monkeys and Microbiomes
- Proposal: identifying contaminated cancer cell lines
- Why anonymous peer review is bad for science
- Data from “The top 50 science stars of Twitter”
- Thoughts on Oxford Nanopore’s MinION mobile DNA sequencer
- poRe: an R package for the visualization and analysis of nanopore sequencing data
- Citations are not a measure of quality
- You’re not allowed bioinformatics anymore
- How not to make your papers replicable
- The lonely bioinformatician revisited: clinical labs
- Comment on Piero Anversa controversy
- We have the $1000 genome; what’s next?
- An improved model for direct to consumer genome sequencing
- How to stand out in academic scientific research
- A Mothur tutorial: what can we find out about the horse gut metagenome?
- Why do we do things?
- Genomics: prepare for the quacks!
- 4-year PhD funding for the development of exome sequencing in pigs
- Biologists: this is why bioinformaticians hate you…
- Is this a realistic portrait of a modern student/post-doc in biology?
- The only core competency you’re ever going to need
- Agreeing and disagreeing with a scientific legend
- Welcome to the $1000 genome
- On cheer-leading and pom-poms
- The UK’s funding for open-access publications is not enough
- Hypocrisy not limited to genomics
- Thoughts on clinical genome sequencing
- The de-democratization of sequencing
- On Quilt Plots, and the need for editorial consistency
- 7 reasons why the NextSeq 500 is a strange choice
- Illumina destroy the opposition again – almost….
- You’re probably not doing metagenomics
- Cats, dogs and bioinformatics
- The car park causation fallacy
- Five things Randy Schekman should have done
- I think you might be a hypocrite
- HPC and biology; a marriage made in hell
- We’re still recruiting!
- A flow chart for feuding scientists
- We didn’t ask for it
- Nanopore wars
- So you want to be a computational biologist?
- Collection of published “guides” for bioinformaticians
- We’re recruiting!
- Genia single molecule sequencing
- I think I might have something magical
- How many hours have been wasted parsing unstructured text in biological databases?
- Are you in peer review debt?
- Should we sequence everyone at birth?
- Food, fantasies and the future
- Why I resigned as PLOS ONE academic editor
- They Were Awful Titles
- How wrong is David Moyes?
- Piledriver in the Cloud
- Bioinformatics is not something you are taught, it’s a way of life
- Bacterial genomes – 2nd and 3rd generation costs
- Five other foods that are like genome assembly
- The KW metric
- Assessing bioinformatics impact
- Examples of the peer review system working
- The $1000 myth
- Traditional media – what’s to like?
- Perhaps there is a chance to change something?
- A quick guide to making your software installable
- Celebrate the people who make your science possible
- A pedantic look at the cost of sequencing
- A guide for the lonely bioinformatician
- Are you ready for the 20% cut in your sequencing budget?
- Don’t tell me this isn’t how I’m supposed to be
- Watson’s law of bioinformatics ontologies
- The alternative “what it takes to be a bioinformatician”
- Shouting at my data in the cloud
- When was the last time you were wrong?
- Dear ENCODE….
- Researchers sequence ancient giant aquatic lizard thing
- The reviewer’s oath
- GATK – why it matters
- Scientific Shakespeare
- Ten things to consider when choosing an NGS supplier
- Call the bioinformatics police!
- Bacterial assembly on MiSeq – power of long reads?
- An embargo on short read alignment tools
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