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 […]
The MacManes Lab at The University of New Hampshire is in search of a PhD student to work on a project aimed at understanding the genomic underpinnings of parental care in the Rock Dove. The successful candidate may have an undergraduate degree in Biology, Computer Science, Statistics, Mathematics, or other disciplines. Interested students are strongly […]
I\’ve been thinking a lot lately about the recruitment of PhD students, given it\’s the time of year when prospective graduate students start looking for labs to join during the next academic year. I\’m keenly interested whenever I see an advert, particularly one of those that list the position as \’fully funded\’. This, coupled with […]
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 […]
Seeking postdoc The MacManes lab at the University of New Hampshire seeks to identify a senior grad student who is interested in working with me on an application to the NSF Postdoctoral Research Fellowship Program (http://www.nsf.gov/pubs/2015/nsf15501/nsf15501.htm), specifically in the “Broadening Participation” part of this program. The MacManes lab is interested in evolutionary genomics, and in […]
I find myself continually frustrated**. Reading transcriptome assembly paper after paper, all of them quality trimming mindlessly at a Phred score 20 or 30. Why do people do this??!?!?! I just don\’t understand, given there is nary a shred of evidence to suggest its benefit, and a substantial amount of evidence to suggest the contrary […]
Earlier in the day, I said this: I don’t think Galaxy/CLC is the solution for biologists with genomic data.. These tools simply allow for sloppy and uninformed analyses. — Matt MacManes (@PeroMHC) August 30, 2014 Now, this is something that I have struggled with for the last few years.. Increasingly, people have been trying to […]
As many of you know, I recently spent a week at MSU\’s Kellogg Biological Station. No, I haven\’t betrayed my Maize and Blue, instead, I was there after being invited by Titus Brown to participate in the 5th installment of ANGUS workshop. I have to admit feeling a fair amount of imposter syndrome going in – […]
CEGMA has been, for my lab, a really great tool for understanding genome assembly completeness and quality, so – that it has had so many problems recently has been a big problem. Never quite sure what exacty the issue is, is revolved around geneid not properly working.. (https://gist.github.com/macmanes/9cb776429df90723e3a9) is an example.. Anyway, to solve this […]
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 […]