Running out of memory on your Mac?

Twice now my mac has run low on memory. When I run omnisweeper the problem is over 50Gb of cores. Found this at https://discussions.apple.com/thread/7852353 The /cores folder is where OS X stores Core Dumps. These are files that are intended for developers to troubleshoot and diagnose faults in their software. They are generated as software … Continue reading Running out of memory on your Mac? →

RNA-seq – how many replicates?

I think we've discussed this paper before in lab meetings, but just thought I'd pop it here for posterity. How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? The authors performed an RNA-seq experiment with 48 replicates per condition, identified the significantly differentially expressed genes, and … Continue reading RNA-seq – how many replicates? →

On the optimal use of methylKit

This is a useful paper from 2017 titled Strategies for analyzing bisulfite sequencing data. It reviews sequencing and alignment approaches, general methylome analysis, differential methylation and annotation, as well as recommending analysis platforms for non-coders. Section 4.1 discusses differential methylation methods, comparing three different methods using a simulated dataset, including as a subset of one method … Continue reading On the optimal use of methylKit →