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 […]
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 […]
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 […]
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 […]