August 6th, 2009
Cofactor has been in business for about 10 months now. In that time we have produced an amazing variety of libraries. Check out a sorted list of them, all 181 as of last week. They span 12 distinct types of libraries. Surprisingly, at least to us, a huge portion of this is RNA. When we were at the genome center, we were really focused on human re-sequencing, but Cofactor’s focus both for software and wet-lab development is now clearly de novo assembly of non-model or emerging-model organisms and their transcriptomes, and expression/splicing/fusion analysis by full-scale RNA-seq.
A quick note about RNA: If you have a larger non-model organism and you would like to begin building genome resources for your work on a tight budget, RNA is a great way to go. You can submit total RNA and after Ribo-depletion or PolyA selection, we can create paired-end Illumina libraries can be assembled into genes. Now exon/exon junctions where there is any alternative splicing will have a gap, but there is still plenty of information to see what genes you have, and even provide a basis for expression work using less expensive single-end reads on the SOLiD mapped back to the assembled transcriptome.
RNA sequencing is like “targeted re-sequencing” that actually works and is actually inexpensive!
June 18th, 2009
Every day is exciting at Cofactor Genomics. Since we posted the new website, we have several pressing announcements!
Our Classroom Project winners have been announced. We are funding 4 undergraduate genomics projects, and some of those even more than the promised 1-lane/1-barcode level. These projects will serve both as experiments in molecular biology and as experiments in education. It is our hope that the syllabi, data, and methods, and perhaps even student testimonials, will serve as templates for undergraduate classes across the nation. Experiential learning is the best way to teach science, especially genomics, and we are proud to contribute to the great work of educators like Sarah “Sally” Elgin and the original Genomics Education Partnership. Several of us at Cofactor either assisted or took Sally’s class, so we encourage you to check it out.
We also launched the long-anticipated Cofactor Video! Bio-Rad and The PCR Song started the fad with Music Videos recast for science geeks. Eppendorf followed suite with a Boy-Band video about the epMotion. Somebody even remade a classic film into The AffyMatrix. Our innovation? Bring science geek-ery to a new genre - the Mock-u-mentary. Enjoy! Force your friends to watch it - that gel extraction can wait.
Last but not least, we can now generate 1 Giga-Base of pass-filter per lane per end on the Illumina using only 60bp reads. If you really wanted 106bp reads, sure then we could give you 1000MB / 60bp * 106bp = 1.8GB per lane per end, but those extra bases aren’t high quality enough to warrant the extra time. Certainly not if you want to put them into something like Velvet where adding more data that is poor quality actually makes the assembly worse. And if you’re not doing de novo assembly, we posit that 60bp is long enough!
Buyer beware! Why do we have this ridiculous expression “pass-filter per lane per end @ 60bp reads” ? These 4 variables all need to be held constant when comparing runs. Many places artificially inflate output amounts by any or all of these methods:
- quoting raw data output instead of filtered (inflates 50-30%)
- quoting output at 106bp reads which are garbage after the ~75th base (inflates 76%)
- quoting output for paired-end lanes when you are thinking single-end (inflates 100%)
- quoting output for an entire flowcell instead of lane-by-lane (inflates 800%)
Of course, when we talk about the SOLiD you have to take it one step further: ”mappable per barcode per end per slide @ 50bp reads.” The SOLiD can run 2 slides at once without really increasing the run time. Since it runs twice a long as the Illumina this conveniently puts it back on par time-wise. Of course, you still get 50% more reads on the SOLiD.
We are always here to cut through the hype of each platform and optimally allocate projects across platforms. Let us know if you have any questions about Next-Gen!
May 11th, 2009
Thank you for visiting the new CofactorGenomics.com!
Please pardon our construction as we transition to the new site. We wanted to make sure to get as much content to everyone as quickly as possible. In the next week we will be adding more pictures, graphs, and reference PDFs all over the site, so make sure to check back frequently.
We are also excited to announce the release of the Cofactor YouTube video on June 5th. Check back then for a link to the new video, and our apologies to Applied Biosystems, Illumina, Qiagen, and Bio-Rad! (You’ll understand when you watch 
)
Finally, don’t forget to get your final entries into the Cofactor Classroom Project! We will be selecting winners soon.
