help…

Posted on 1 CommentPosted in Bioinformatics

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 […]

Shot down..

Posted on 8 CommentsPosted in Uncategorized

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 […]

Shannon Stream of Consciousness…

Posted on 6 CommentsPosted in Bioinformatics, Publishing, software

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 […]

NGS Summer 2016 – Analyzing Next-Generation Sequencing Data

Posted on Leave a commentPosted in Bioinformatics, Illumina, software, tenure track

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 […]

Using OrthoFinder

Posted on Leave a commentPosted in Bioinformatics, software

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, […]

Feeding your Transcriptome with the Oyster River Protocol

Posted on Leave a commentPosted in Bioinformatics, Publishing

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 […]

I will never understand

Posted on Leave a commentPosted in Publishing

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 […]

PALADIN: software for rapid functional characterization of metagenomes

Posted on 1 CommentPosted in Bioinformatics

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 […]