tl;dr: no I was talking with my grad student, Lauren Kordonowy yesterday about if error correction should be done to reads prior to abundance estimation. I said no, but told her to do the experiment to convince herself. Now: n=1 and all that, but her results are unequivocal. We used Salmon quasi mapping as implemented […]
Lazy web query. Actually not that lazy given I did google. Maybe this seems like a silly problem that I should be able to figure out.. Anyway, I want to download a bunch of sequences from UniProt. I have a URL that works http://www.uniprot.org/uniprot/?&format=fasta&limit=5&query=taxonomy:6656+AND+name:ABCC11 which in this case will download all the Arthorpod sequences for […]
I’ve been working on a head to head comparison of the de novo transcriptome assemblers Trinity v.2.2.0 versus the new kids on the block – Shannon and BinPacker. The tl;dr version of the post is that these new assemblers are very good, and should be considered for new assembly projects, with just a couple of […]
I’m trying (still) to get my manuscript on transcriptome assembly best practices published. I\’m sorry to say that it is not going that well.. It seems that there is a disconnect between editors (who mostly hate it) and people actually assembling transcriptomes (who find it very valuable). How to reconcile these differences.. Here is the […]
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 […]
August 8 – August 19th, 2016 Kellogg Biological Station, Michigan State University To Apply: Fill out the form here: http://goo.gl/forms/jWE6fx4WP0. Due date 3/1/17 Course Directors: Matt MacManes, Assistant Professor, University of New Hampshire (@macmanes or matthew dot macmanes at unh dot edu) Meg Staton, Assistant Professor, University of Tennessee, Knoxville (@hardwoodgenomic or mstaton1 at utk […]
I\’ve been working on a project where I need to identify orthogroups – We used to use OrthoMCL for this, but it\’s very slooow. When I read a few months ago about OrthoFinder (http://www.genomebiology.com/2015/16/1/157, https://github.com/davidemms/OrthoFinder) I was pretty stoked cause it was faster and just as accurate or more. I\’ve run into a few issue, […]
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 […]
At long last, I\’d like to introduce PALADIN, software created by a group of UNH researchers (Anthony Westbrook – the lead developer, Jordan Ramsdell, Taruna Aggarwal, Louisa Normington, Dan Bergeron, Kelley Thomas and myself). It allows for rapid functional characterization of meta-communities using a mapping approach **. It is available at https://github.com/twestbrookunh/paladin, and go there […]