Should we change the threshold for statistical significance? Many think so ..

There is a new preprint that was posted recently in the PsyArXiv that may (or even should) be of interest: Redefine statistical significance by Benjamin al. One sentence summary from the authors: We propose to change the default P-value threshold for statistical significance for claims of new discoveries from 0.05 to 0.005. First page or so: …

Could be interesting: The Metagenomics MVP Challenge v1.0

Source: NIST Challenge — CosmosID – Exploring the Universe of Microbes This could be interesting.  NIST & COSMOS ID and ABRF are conducting a metagenomic sequencing methods challenge. From their site: When using metagenomic methods to assess the content of a complex microbial sample, there are many steps in the measurement process where bias might …

WTH is ILR?

WTH is ILR? by Alex Washburne & Jamie Morton Jamie and I have penned a popularization of the isometric log-ratio transform with the intention to allow non-mathematicians to understand the intuition behind what it is, why we use it, and how different methods use the same tool in different ways. The full write-up is available …

Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies

So I had two thoughts when I read the article title “Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies“… #1:  Ack!  Yet another thing to worry about in the insanely complicated craziness that is 16S amplicon sequencing. #2: I probably shouldn’t be the person to blog about this because I’ve honestly never …

microBEnet journal club: MetaBAT for reconstructing single genomes from complex microbial communities

    There is an interesting paper out a few days ago in PeerJ: MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. By Dongwan D. Kang, Jeff Froula, Rob Egan, Zhong Wang​.  The key to what they do in the paper is summarized in Figure 1:   The legend is below: There are three preprocessing steps before MetaBAT is …

Best practices for sample processing and storage prior to microbiome DNA analysis freeze? buffer? process?

So – we have been having a running discussion with people in my lab about one key issue in microbiome studies – how does one store samples prior to doing DNA extractions and does it matter?  As background for those who do not do this kind of work – the general principle behind DNA based …

Genomic data sharing via BitTorrent, part 2 – BioTorrents to BitTorious

As someone who uses sequence data for most of my research,  I am continually happy with the fact that sequencing continues to get cheaper and easier and faster and bigger and better and more and more and more.  Along with such continued advances, sharing the data produced by such sequencing has become somewhat challenging at …