Single cell extravaganza

AGBT had lots of presentations on both clinical and single-cell work last February and on Wednesday, February 12th Aviv Regev, of the Broad Institute described her groups experience with the Fluidigm C1 system, and their early work in understanding cell-to-cell communication in the immune system. The results were published in Nature a couple of days ago. A more exciting story for me scientifically was published by Aviv Regev and Bradley Bernstein in Science awhere they describe the use of single-cell sequencing to understand tumour heterogeneity.

The big headlines for me were that just 1M RNA-seq reads were enough to get high-quality gene expression estimates, and that single cells are great: but we’re going to need lots of them to delve deeply into biological systems. Both papers showed a massive loss of data at QC stages, around 1/3rd of cells were lost and only 30% of reads mapped to the transcriptome. Hopefuly both of these are things we can improve in the next few years to make single-cell mRNA-seq even more powerful.

Dear Santa (read Jay Flatley)

How may days till Christmas...

New sequencers from BGI: are they going to take market share from Illumina et al

Everyone knows BGI bought Complete Genomics last year. What is less clear is what BGI's plans are for Complete's platform (a little more at the bottom of this thread). There has also been a bit of buzz about seqeuncers being developed by the genomics institute actually in Beijing. Two recent articles on Chemistry World and Firecebiotechit discuss a newly developed sequencer coming out of the Beijing Institute of Genomics. It may even be in the hands of alpha testers now but my lab is not one of them - BIG: feel free to get in touch!

V4some: 1TB here we come…

Our HiSeq 2500 v4 validation runs are just about to finish and I thought I’d share some details. Ideally I’d give you access to the runs so you can dig around yourselves but until Illumina makes this possible on a per lane basis in BaseSpace you’ll have to make do with my plots.

Look how far we've come

Agilent tools to help with your NGS pooling

Pooling samples for multiplexed sequencing has become the norm for many researchers, especially in the light of 1TB sequencing in 6 days! However many users struggle to get pools nicely balanced. I've just seen a tool I think is helpful so I thought I'd share it with you.

Forget the $1000 genome; a house in Cambridge costs more than the 1000 genome project!

I had a chat with a colleague about the insanity of the Cambridge property market and determined that a house here could cost more than the 1000 genomes project. In theory this would cost $1,000,000 if run on HiSeq X Ten today and only take 20 days to sequence, both phenomenal achievements all made possible by the magic Illumina have worked on SBS chemistry.

If only they could magic the Cambridge property market back to somewhere sensible. A Rightmove search in CB3 9HY for houses finds just five available in a 1 mile radius of the number 2 best place to live in the UK. Newnham in Cambridge is a nice place to live offering “country living in the heart of Cambridge”, with a “genuine village atmosphere”, good shops, and good schools. But the cheapest house available is £750,000 or $1,260.000 for 1,407 sq ft, 2 bedrooms and planning for a house in the garden!

Why no PhiX on BaseSpace: %Q30 vs error rate, should you choose between them

We just had a shiny new NextSeq installed and the validation run gave 480M reads (about 20% above the spec of >400M reads) and 83.1%Q30 (against Illumina's spec of >75%Q30 at 2×150bp). But the initial reaction internally was that the error rates looked too high meaning we were likely trim back to 100bp. The validation run showed error rates of 0.22%, 0.37%, 0.43% at 35, 75 and 100bp respectively, and about 4% at 150bp.

What should we call an overlapping read-pair from a paired-end fragment run?

HiSeq rapid is going to be getting paired-end 250bp reads. Assuming you can sequence with a 500bp insert (+/-50bp) then we can expect to get perhaps 200-300M pairs of overlapping reads that can be merged to create 200-300M 500bp sequences. I suspect this is going to have a transformative effect on genome assembly and transcript isoform detection and the development of novel methods is likely to come from longer and longer reads on the Illumina platforms.

NASA's NextSeq?

A wonderful story appeared on BBC news website today about the company Planet Labs who are using a similar idea Illumina implemented in designing NextSeq - borrow from consumer electronics to advance science. Rather than building sequencers Planet Labs have built and launched a flock of 28 shoebox-sized "cubesats" - cheap, miniature imaging satellites. This is GoogleMaps satellite images with super-high resolution.