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 […]

11 05, 2017

Update on @illumina index-swapping: better libraries

By | May 11th, 2017|Categories: Methods and applications, Next-generation sequencing|Tags: |3 Comments

Index-swapping appears to be driven by excess adapter/primer (Illumina whitepaper). The take-home messages are 1) to use UDIs (unique dual-indexes), and 2) clean-up your libraries to remove left-over adapter/primer. Later in this post I’m going to work through one solution for getting rid of any remaining adapter/primer in an NGS library; but […]

5 05, 2017

Running @nanopore RNA-seq in a core lab

By | May 5th, 2017|Categories: Core facilities, Nanopore sequencing|Tags: |0 Comments

This is a first for me as I’ve not finished this post at all! Instead I’m going to use this as a space to document my ideas, and experiences, in bringing Oxford Nanopore’s RNA-seq into my core lab at the CRUK Cambridge Institute. I’m hoping […]

5 05, 2017

Inflection points for @nanopore sequencing

By | May 5th, 2017|Categories: Methods and applications, Nanopore sequencing, Next-generation sequencing|6 Comments

When will nanopore sequencing push short-reads (i.e. Illumina) off their pedestal? According to Clive PromethION is the Illumina killer…but this same conversation was going on many times at London Calling. I wanted to highlight two areas that might be about to flip to ONTs advantage […]

4 05, 2017

London Calling: day 1 update from @nanoporeconf

By | May 4th, 2017|Categories: Conferences, Nanopore sequencing|Tags: |3 Comments

I’m excited to be at ONTs London Calling event today and tomorrow. Expect to see lots of coverage on Twitter. Missed the workshop yesterday or want a late preview of what’s coming then head over to Keith’s OmicsOmics blog. Update: coverage from @Gringer, ONT, NextGenSeek (storified […]

24 04, 2017

Update on @illumina index-swapping: better barcode design

By | April 24th, 2017|Categories: "Experimental design controls etc", Core facilities, Methods and applications, Next-generation sequencing|Tags: , , |2 Comments

Last week I followed up on the index-swapping issue after Illumina released their white paper and also covered what Ethan Linck at The Molecular Ecologist had posted about the Sinha et al BioRxiv paper. In that post I said I’d write a follow-up post about index design over the weekend – here it is! […]

21 04, 2017

Update on @illumina index-swapping

By | April 21st, 2017|Categories: "Experimental design controls etc", Core facilities, Design, Methods and applications, Next-generation sequencing|0 Comments

Illumina released a white paper this week describing their efforts to understand the index-swapping issues with the ExAmp chemistry. This story has been covered many times and got lots of Tweets in the days since the BioRxiv paper from Stanford was uploaded. Megan Molteni at Wired wrote a lengthy […]

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 […]

Load More Posts