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 […]

We\’re headed to Evolution 2014!! Excited to see old friends and meet new ones!! Here is a list of talks and posters by MacManes lab members.   Saturday Poster Session Date: Saturday, June 21, 2014 Time: 7:00 PM – 9:00 PM Comparative Genomics of Desert Adaptation Among Mice in the Genus Peromyscus  Lauren Kordonowy, University […]

I am working on a genome assembly- this is a human sized vertebrate genome (Peromyscus eremicus). I work on this species in the context of adaptation to deserts (e.g. extreme heat and aridity), and in the future on its behavior. Aside from the biological goals, I’m interested in showing that large genome assembly projects don’t […]

Yay– the day has finally come to release TAMrS- (T)ranscriptome (A)ssembly (M)ade (r)eally (S)imple! TAMrS is a pipeline that produces transcriptome assemblies from a set of PE or SE reads, importantly, using a single command. The goal of this software project is to allow non-bioinformaticians/non-programmers to use cutting edge tools (e.g. Trimmomatic/FLASH/Trinity/eXpress) that are typically […]

I was pointed to a new paper in PLOS ONE: An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis. Their central thesis seems to be this: \”….trimming is beneficial in RNA-Seq, SNP identification and genome assembly procedures, with the best effects evident for intermediate quality thresholds (Q between 20 and 30). This it […]

Is there anybody out there– running a Linux distro other than Ubuntu– can you download and install some new software I’m writing. I want to make sure it works on other Linux distros.. The software pipeline aims to drastically simplify transcriptome assembly- input PE or SE fastQ files, out pops an assembly and estimates of […]

I am really loving bwa mem-it is a fast and accurate short read mapper.. One problem, unlike bowtie/bowtie2, there are no alignment stats printed by default at the end of the run.. This is a major annoyance, as I (and I suspect everyone else) uses these stats to infer something about the quality of the […]

I recently served on an NSF panel, and although I’m apparently not supposed to share the details of which panel and when, It seems like a good idea to share my experiences. I left feeling strangely comforted. Yes- funding rates are 5%, and this means that some very good science gets left unfunded.. But the […]

I updated my brand new iMac to Mavericks yesterday AM- since then, I’ve been having intermittent problems with the keyboard and mouse freezing. Te computer remains responsive (emails being received, can ssh into machine), its just that the input devises are non-functional. This happened 5x yesterday, including once overnight when the computer was resting. I […]

A group of us on Twitter got to talking about online office hours..  Like usual, it started simple @hylopsar I’ll admit this this is largely @eperlste’s idea, who, I think, is working on an implementation using google hangouts.. — Matt MacManes (@PeroMHC) September 19, 2013 This was followed up with Freshly minted assistant professor @PeroMHC […]