April’s Webinar featured Jingwei Song of the Virginia Institute of Marine Science and his work in phenotypic plasticity in spotted seatrout. Much of this work relied on a de novo transcriptome assembly, and a lot of differential expression (DE) work afterwards. Since we highlighted our tools for the assembly last month, let’s focus on DE this month!
If you are interested in other upcoming talks, please register here.
Starting your own differential expression project
If you are interested in doing similar work with differential expression, we can help you get started with some resources below.
Background information worth checking out:
NCGAS video on some quick theoretical background. We cover some vocabulary (false negatives, false positives, FDR) and the most common question we get – “which software should I use to generate counts and which software should I use to determine differential expression?”
Wonderful set of inter-related papers that we refer to in the above talk. These discuss different software and how they interact with sample size, level of sensitivity, preference on false positive/false negative balance, etc. Costa-Silva et al 2017, Schurch et al 2016 (referenced the most of the three), Schurch et al 2015 (very extended version of the 2016 paper)
Community tools for your project:
Trinity’s really well-made wrapper scripts for handling differential expression. These are the scripts we use in our recommended workflow, so this documentation is very helpful for doing tweaks, for visualizing time series, and for creating clusters.
Our DE workflow for working with de novo assembled transcriptomes, and our DE workflow for genome-guided mapping of reads. Both of these use trinity’s differential expression wrappers, but generate counts matrices differently.
Support while you work on your project:
Monthly help desk: We are launching a monthly help desk to provide live help and discussion for the monthly webinar topic and anything you are stuck on in bioinformatics. This will take place every fourth Tuesday of the month from 2-4pm EST and will be held through Discord (ncgas.help.desk, please email firstname.lastname@example.org for an invitation email or if you are not on our mailing list!)
One-on-one consulting & troubleshooting: email email@example.com