A new transcriptome assembler has been released. Shanon: http://biorxiv.org/content/early/2016/02/09/039230 and http://sreeramkannan.github.io/Shannon/. It looks quite interesting from an algorithm standpoint and claims to be better than the existing suite of assemblers.. Good deal, I\’m all ears! I\’ll hope to provide a full review (with the lab) in a bit, but I have a few immediate suggestion after kicking […]
After months of work, my new manuscript \”An opinionated guide to the proper care and feeding of your transcriptome\” is out on bioRxiv!! Accompanying this is a living document – the version controlled and updated set of current best-practices \”Oyster River Protocol for Transcriptome Assembly\”. These documents serve to provide evidence-based guidelines for de novo […]
begin{rant} I will never understand why it takes bioRxiv so many hours to \’screen\’ a preprint. Here are some solutions. Ask for volunteer screeners. These are people that have already submitted preprints to bioRxiv in the past, and therefore are \’trustworthy\’. As I\’ve said in the past – I\’d volunteer. Even if people screened a […]
So last night I discovered an extremely interesting paper, \’The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima\’ by Richards and colleagues. After reading the abstract, for genomics papers I always read the methods sections next. I like to know how the authors did what they […]
I am writing this, in hopes that it will remind people (reviewers) of the critical details required of published transcriptome studies. This guide intends to cover the details through the production of the final transcriptome assembly. I will write about testing for differential expression at a later date. The ‘living document’ available for editing is […]
God people, this is not that hard.. If you are working in academia, in the US, you are very likely to be funded by taxpayer money. The data you produce is enabled by taxpayers- all (most) of us.. So why is is such a hard friggin’ concept that you should be required to share your […]
I was looking at the Assemblathon2 paper in Google Scholar, lamenting the fact that it is still not properly indexed when I got to noticing something funny- the number of citations the paper has received varies depending on whose page you are looking at. 3 different pages, 3 different numbers of cites.. I wonder which […]
I just got done uploading a manuscript to the PeerJ Preprint server. It was awesome! This was a manuscript that was outside even the loosest of definitions of quantitative biology, and therefore not appropriate for arXiv. I am really keen to see biologists using preprint servers, and up until now, where to send non quant. manuscripts was a […]