Complete Khoisan and Bantu genomes from southern Africa : Article : Nature

http://www.nature.com/nature/journal/v463/n7283/full/nature08795.html

Just attended a very good lecture by Stephan Schuster, entitled "African Genomes: Charting Human Diversity"

He offered unbiased views / charts on the platform differences between 454, GAIIx, HiSeq, SOLiD for NGS sequencing coverage (which I think I should not repeat here). It points to the need to do sequencing on 2 different platforms to get a more accurate SNP list.

He also gave compelling reasons for getting a 20x coverage of Human genome done in 454 to complete the human genome (457 gaps in hg19). 

Yes, I often forget that the media / lay person thinks that the human genome is 'complete'. It's a often ignored 'secret' that actually it isn't. Maybe the next marketing ploy(i mean strategy) for emerging sequencing platforms would be to be THE ONE that actually finishes the human genome.

Guide/tutorial for the analysis of RNA-seq data

link in seqanswers

Excellent starting point for those confused about the RNA-seq data analysis procedure.

Hello,

I've written a guide to the analysis of RNA-seq data, for the purpose of differential expression analysis. It currently lives on our internal wiki that can't be viewed outside of our division, although printouts have been used at workshops. It is by no means perfect and very much a work in progress, but a number of people have found it helpful, so I thought it would useful to have it somewhere more publicly accessible.

I've attached a pdf version of the guide, although really what I was hoping was that someone here could suggest somewhere where it could be publicly hosted as a wiki. This area is so multifaceted and fast-moving that the only way such a guide can remain useful is if it can be constantly extended and updated.

If anyone has any suggestions about potential hosting, they can contact me at myoung @wehi.edu.au

Cheers

Matt

Update: I've put a few extra things on our local Wiki and seeing as people here seem to be finding this useful I thought I'd post an updated version. I'm also an author on a review paper on Differential Expression using RNA-seq which people who find the guide useful, might also find relevant...

RNA-seq Review

A scientific spectator's guide to next-generation sequencing

ROFL
I love the title!

A scientific spectator's guide to next-generation sequencing

Dr Keith not only looks at next gen sequencing but also the emerging technologies of single molecule sequencing. Interesting read!

My fave parts of the review
"Finally, there is the cost per base, generally expressed in a cost per human genome sequenced at approximately 40X coverage. To show one example of how these trade off, the new PacBio machine has a great cost per sample (~U$100) and per run (you can run just one sample) but a poor cost per human genome – you’d need around 12,000 of those runs to sequence a human genome (~U$120K). In contrast, one can buy a human genome on the open market for U$50K and sub U$10K genomes will probably be generally available this year."

"Length is critical to genome sequencing and RNA-seq experiments, but really short reads in huge numbers are what counts for DGE/SAGE and many of the functional tag sequencing methods. Technologies with really long reads tend not to give as many, and with all of them you can always choose a much shorter run to enable the machine to be turned over to another job sooner – if your application doesn’t need long reads."

 

 

Cheaper Next Generation Sequencing?

The biggest barrier to NGS is always the cost. Roche has a nice idea to bring down cost by downsizing their machines. But I wonder how many people need a NGS machine that shortcuts on the volume of data.