I was an early user of Tophat, way back before there were many good tools for quantitating expression from NGS reads. I was just learning how to process these types of data (e.g., learning a scripting language), so I thought that many of the problems I encountered were a result of my inadequacy — and […]
God people, this is not that hard.. If you are working in academia, in the US, you are very likely to be funded by taxpayer money. The data you produce is enabled by taxpayers- all (most) of us.. So why is is such a hard friggin’ concept that you should be required to share your […]
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 […]
I was looking at the Assemblathon2 paper in Google Scholar, lamenting the fact that it is still not properly indexed when I got to noticing something funny- the number of citations the paper has received varies depending on whose page you are looking at. 3 different pages, 3 different numbers of cites.. I wonder which […]
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\’ve just finished work on a new On the optimal trimming of high-throughput mRNA sequence data, which is as a preprint on bioRxiv: http://biorxiv.org/content/early/2013/12/23/000422. The paper has been submitted to Frontiers in Bioinformatics and Computational Biology for potential inclusion published in a special issue dealing with the Quality Control of NGS data (http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00013/abstract). I began work on […]
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 […]