Friday, 17 October 2014

Your own personal genome project

I was chatting with a colleague at work who'd asked me if I know anywhere they could get their genome or exome sequenced. My genome has been sat in the freezer for over five years wanting to go onto a flow cell, but I've never been comfortable putting it on our own machines. I did get 23andMe'd a few years ago but they've closed the exome for now.

Today there are many sequencing service providers across the world. Would any of them be open to a consumer led project? How many genomes/exomes would we need to sequence to get a price consumers were willing to pay? To test the market we've used AllSeq: "the global sequencing marketplace", and a couple of replies have now come in!

Thursday, 9 October 2014

Twitterbots for NGS

I've been inspired to create three Twitterbots for NGS papers on @RNA-seq, @ChIP-seq and @Exome-seq by Casey Bergman at the University of Manchester. I'd not come across Caseys twitter account (I don't actually use Twitter that much) or his lab website and blog; but I was directed there by a piece on the Nature website...How to tame the flood of literature.

What Casey has done is pretty simple and it is very well explained in his blog post, or by Rob Lanfear who has posted instructions on GitHub. There are three simple steps for PubMed and Twitter (and more for arxiv, peerj, etc).
  1. Set up a twitter account
  2. Set up a pubmed search
  3. Set up your account
The feeds I created only went live this evening and I'll follow Robs advice to refine them over the next few weeks. Let me know if you like them, and why not create your own feed.

PS: Casey has a great post on how to host a custom UCSC genome browser trackwith Dropbox.



Tuesday, 7 October 2014

Count-down to AGBT 2015

Registration is open! The registration process for AGBT has been overhauled in the last few years; yes there's still a lot of people who don't get in, but it seems to be pretty fair. 

I hope to see you there. I'm going to be blogging and Tweeting again (assuming I get in). Say Hi if you read CoreGenomics and I'll buy you a beer (or rather grab one from Illumina, Agilent, etc)!

Thursday, 2 October 2014

Whole exomes from single cells: Fludigm C1 update

This was not a planned post but it follows on nicely from today's other one about exomes. This time I'm writing about Fluidigm's new single-cell exome-seq protocol. Yup that's right, whole exomes from 96 single cells! The C1 is an amazing piece of kit (wish I had one) and we've used it a little bit for mRNA-seq. The ability to sequence single-cell genomes and exomes means you can pretty much do whatever you want with a single-cell now. So how do the exomes look?

More on exomes

I've been finding out more about exomes: specifically QC analysis using HS Metrics in Picard. There's loads of useful metrics and I'm hoping to get to a point that I can explain these to users here and also look at the results to try and troubleshoot an experiment. I'm also trying to understand what sort of read length we should be using for exome analysis. An earlier post discussed my thoughts around moving to PE125 or switching to SE125 and running more lanes. In a follow up post (watch this space) I'll try to consider the impact of different run modes: will users/reviewers accept any kind of read for an exome or will they baulk at seeing something different from the paired-end norm?

PS: Your comments on this would be greatly appreciated!