3 01, 2018

NGS methods naming discussed in Nature Methods

By | January 3rd, 2018|Categories: Methods and applications, Next-generation sequencing|0 Comments

I’m really pleased to have a commentary article published in Nature Methods today: A profusion of confusion in NGS methods naming. My colleague Jaques Retief and I have been talking about NGS methods for many years and decided to write this article to highlight some of […]

18 12, 2017

Why are @illumina flowcell names so similar (but only occasionally rude)

By | December 18th, 2017|Categories: Next-generation sequencing, Other stuff|2 Comments

Anyone who’s run Illumina instruments over the years is likely to have noticed how flowcells can have remarkably similar (and occasionally amusing) names. This can create a real headache when looking for a specific run as a single mismatch can cause you to spend some time […]

24 11, 2017

SPLiT-Seq: single-cell RNA-Seq without the hardware

By | November 24th, 2017|Categories: Methods and applications, Next-generation sequencing, Single-cell sequencing|Tags: , , |0 Comments

I’ve been meaning to write up a post on a BioRxiv report from earlier this year: “Scaling single cell transcriptomics through split pool barcoding”1. The Seelig Lab at the University of Washington have developed a single-cell RNA sequencing method to enable labelling RNA molecules with cell-of-origin information using […]

8 11, 2017

Error-corrected ctDNA sequencing for mutation and CNV using UMIs

By | November 8th, 2017|Categories: ctDNA, Exomes and amplicons, Methods and applications, Next-generation sequencing|2 Comments

A recent BioRxiv report from the Gerlinger group at ICR describes a targeted ctDNA sequencing method that uses error correcting UMIs to achieve 100% sensitivity for mutant allele frequencies of >0.15%, and 87% at >0.075%, and reduce false-positive mutation calls by 98.6%, without adversely affecting the […]

7 11, 2017

R vs Excel by @vivalosburros

By | November 7th, 2017|Categories: I am not a Bioinformatician, Methods and applications, Other stuff|0 Comments

In this post I wanted to highlight the wonderful “Excel vs R: A Brief Introduction to R”  by Jesse Sadler. This is full of useful and practical advice on using R in place of Excel (or any other spreadsheet) for simple data analysis. I use […]

19 10, 2017

@Illumina Nextera Flex

By | October 19th, 2017|Categories: Exomes and amplicons, Library Prep, Methods and applications, Next-generation sequencing|1 Comment

My lab has been a long-time user of Illumina’s transposase exomes for the very simple reason that the 50ng input has been the lowest on the market for number of years*. This made it attractive for cancer samples where we are really limited on DNA availability; […]

16 10, 2017

WGS of HPV reveals the finer details of HPV genetic variation

By | October 16th, 2017|Categories: Methods and applications, Next-generation sequencing, Uncategorized|0 Comments

Because HPV has such a small  and relatively simple genome (8,000 bp encoding 8 genes) it is possible to screen for genetic variation that may underly carcinogenesis. A team from the National Cancer Institute (NCI) has just published the sequencing of over 5,570 human cell and tissue samples – […]

12 10, 2017

Who’s the scientific equivalent of Harvey Weinstein?

By | October 12th, 2017|Categories: Other stuff|0 Comments

The news about Harvey Weinstein can hardly have escaped the attention of even the most lab-bound post-doc ro PhD student. The investigative journalism at the The New York Times story has led to the downfall of a movie mogul for sexual harassment, unwanted physical contact and other things most of us […]

5 10, 2017

Posting Enseqlopedia content to LinkedIN

By | October 5th, 2017|Categories: Uncategorized|0 Comments

Hopefully this post is going to pop up as if by magic to all my LinkedIn contacts. This is something I’ve been meaning to do for ages and finally had a go. Thanks to the people at WPBeginner for writing this “how to guide” to make […]

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