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 – […]

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 […]

10 07, 2017

Cancer amplicon nanopore sequencing

By | July 10th, 2017|Categories: Uncategorized|0 Comments

Prof Yutaka Suzuki’s lab at the University of Tokyo published a paper last week in DNA research: Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer. In the paper they described their work detecting SNVs in EGFR, KRAS, NRAS and NF1, and EML4-ALK, […]

22 05, 2017

#singlecell seance at the Earlham Institute

By | May 22nd, 2017|Categories: Uncategorized|0 Comments

Iain Macaulay organised a #singlecell meeting at Norwich’s Earlham Institute earlier this month. The meeting was fun and there were some great presentations during a day of talks and discussion on the development and application of single cell technologies. 100+ #singlecell analysis methods at www.tinyurl.com/mqabyur One that […]

10 04, 2017

Index-swapping with @illumina ExAmp clustering

By | April 10th, 2017|Categories: Uncategorized|8 Comments

A paper uploaded to BioRxiv yesterday is the first (almost) published report of index-swapping on Illumina’s Exclusion-Amplification (ExAmp) chemistry. The paper: Index Switching Causes “Spreading-Of-Signal” Among Multiplexed Samples In Illumina HiSeq 4000 DNA Sequencing, by a group from Stanford Functional Genomics Facility published a re-analysis of single-cell […]

22 03, 2017

10X Genomics 10x cheaper…and better too!

By | March 22nd, 2017|Categories: "Experimental design controls etc", 10X Genomics, Methods and applications, Next-generation sequencing, Single-cell sequencing, Uncategorized|0 Comments

Confession: this post may not actually make your 10X Genomics experiments ten times cheaper…but implement Demuxlet in your workflow and with the right sort of experiment you might just get there! Single-cell RNA-Seq might just have got a whole lot cheaper, thanks to a method […]

8 03, 2017

Really long reads on @nanopore MinION

By | March 8th, 2017|Categories: Uncategorized|Tags: |0 Comments

The Oxford Nanopore MinION is generating some truly staggering read-lengths. Keith Robison has summarised many of the major advances of the past few months; MinKNOW increasing yield by reducing pore blockage with a “nano-Heimlich manoeuvre” which increases yields to 10Gb (ONT’s CSO Clive Brown has self […]

10 01, 2017

Illumina NovaSeq and other news

By | January 10th, 2017|Categories: Uncategorized|0 Comments

I’m not in tomorrow as I’m off to a funeral so I’ll not be writing anymore about the new sequencer from Illumina till later in the week. But here’s my initial thoughts… Illumina’s presentation at JP Morgan is over and they’ve certainly delivered. NovaSeq is the latest […]

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