Short comments on Nature's new open-access initiative

Nature announces a new open-initiative that allows any subscriber individuals and institutions to share a public-access link to Nature articles (http://www.nature.com/press_releases/share-nature-content.html).

It is a good, but small, step forward, although the intention of Nature is still to maximize their revenues from subscription business.

I would also encourage all authors to "self-archiving" their papers / manuscripts on their personal or institutional websites, which will make their work widely available and promote open access. The six-month limitation of Nature only applies to the finalized version, and it is legal to self archive the original manuscripts any time at the authors' wish (http://www.eprints.org/openaccess/self-faq/#self-archiving-legal).

Using UCSC Genome Browser Sessions to Organize and View MethBase Tracks

I would like to share a tip that uses the UCSC Genome Browser Sessions to organize and view MethBase tracks.

As of 03/18/2014, MethBase contains 2294 tracks, including tracks for methylation levels, read depths, HMRs, etc. For human alone, there are 1130 tracks. Since each one may be interested in different set of samples and different selection of features, and want to display them with specific settings, there is no single setting that satisfies everyone. Fortunately, the UCSC Genome Browser Sessions provides a nice feature for you to 1) manually tailor a set of tracks (e.g., brain related), 2) store them for future re-use, and 3) share them with others. With UCSC Genome Browser, each one will have a "personalized" view of MethBase.

Using the Session feature requires you to create an account with UCSC Genome Browser and is quite straightforward (http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html). For example, here is a UCSC browser session that contains high coverage methylomes of normal cell samples from human (link).

Hopefully, more interesting and useful sessions, such as brain development oriented and cancer oriented, will be created and shared.

A Survey of Commercial Providers of Whole Genome Bisulfite Sequencing Services

These days I am working on an NIH proposal that involves whole genome bisulfite sequencing (WGBS). For the purpose of project budgeting, I surveyed several commercial providers of WGBS. The following list of companies provide WGBS service, including library preparation and high through sequence with Illumina machines. Most of them also provide additional bioinformatics service as well. Our project only requires library preparation and sequencing services, the quote from the lowest to highest are: BGI < SeqWright < NXT-dx < Glocal Biologics < Alpha Biolaboratory < ACGT. Illumia only offers service if the desired coverage of a single sample is above 30x, and I have not heared back
from Zymo Research yet.

• BGI Americas http://bgiamericas.com
• Zymo Research http://www.zymoresearch.com/
• SeqWright http://www.seqwright.com/
• NXT-dx http://www.nxt-dx.com/
• Illumina http://www.illumina.com/index-c.ilmn
• Alpha Biolaboratory http://alphabiolab.com/
• Global Biologics http://www.globalbiologics.us/
• ACGT Inc http://www.acgtinc.com/