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 […]
People!!! Google scholar seems to be having problems with papers are originally indexed as arXiv preprints, then go on to be published elsewhere. e.g. a journal. Google Scholar seems to ignore the new (real) citation, and be stuck with the arXiv submission- Has anyone else experienced this issue? Case in point: A new paper I […]
Known to some of you, I recently accepted a tenure track position at the University of New Hampshire in their Department of Molecular, Cellular, and Biomedical Sciences.. I was helped immensely by my Twitter and blog friends (especially this set of posts), and this is my attempt at paying it forward. I’d really like to […]
In my continuing quest to conquer fastQ, fastA, sam & bam files, I have accumulated several useful ‘tools’. Many of them are included in other software packages (e.g. SAMtools), but for some tasks, especially file management and conversion, no standard toolkit exists, and instead researchers script their own solution. For me, sed and awk, along […]
Instead of trying to squeeze this explanation into 140 characters, here is a short blog about the issue. I’ve posted the question to the samtools list serve, but no response there. I am generating consensus sequences from a series of BAM files using the standard samtools command: samtools mpileup -AIuf my.fasta my.bam | bcftools view -cgI […]
I just got done uploading a manuscript to the PeerJ Preprint server. It was awesome! This was a manuscript that was outside even the loosest of definitions of quantitative biology, and therefore not appropriate for arXiv. I am really keen to see biologists using preprint servers, and up until now, where to send non quant. manuscripts was a […]
OK, so I have been fighting with GREP all afternoon– Im about to kick it in the teeth! Somehow, there are more lines in my output file than in my subject file.. This is driving me crazy cause I can’t figure out why!!!! Here is the simple enough command: query.txt | sort -k1 | awk […]
I am writing this blog post in support of a paper that I have just submitted to arXiv: Improving transcriptome assembly through error correction of high-throughput sequence reads. My goal is not to talk about the nuts and bolts of the paper so much as it is to ramble about its motivation and the writing process. […]
Every once in a while I get a spam message that is cooler than average– this one is, mainly because somebody took some time to add a few more details about the ‘mystery box of money’ than usual. For instance, Mark Morgan, who is the FBI agent named in this email, is actually a FBI […]