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 […]
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 […]
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! […]
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 […]
The Helios/CyToF mass-cytometry technology is making waves here in our Flow Core and is likely to be a useful addition to multi-omic studies. Fluidigm have a series of webinars that I thought readers of Core-Genomics might be interested in: Decoding human tumors and healthy tissue […]
This post is a follow on from my ABRF2017 presentation this morning. Slides are available on SlideShare. RNA-Seq is the most widely published NGS method, but what do researchers mean by the term “RNA-Seq”? Virtually none of them mean sequencing of RNA. Most are talking […]
Long-reads require long DNA molecules which require high molecular weight (and undamaged) DNA. Extraction with your standard column is unlikely to be optimal. I’m starting to look at the best methods for HMW DNA extraction for long-read applications as my lab is supporting a couple of […]
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 […]
Two publications presenting really cool technologies recently caught my attention: “Lego for molecular biology” and “CATCH-Seq: CRISPR for target enrichment sequencing”. Both are technologies I’d like to play with, and my son can join in the Lego modelling if we build some here in Cambridge! Lego […]
A paper published one month ago in Nature Genetics: Stessman et al 2017, by Evan Eichler’s group at HHMI, reported finding 91 genes associated with neuro-developmental disorders. 25 of these were enriched in autism probands and the authors reported a “network associated with high-functioning autism (full-scale IQ >100)”. […]
