In March 2021 we started a webinar series featuring research supported by our resources! We hope this becomes a regular means for our community to interact… sharing how the research community uses our resources means that you can build off each other’s successes.
Our first speaker was Dr. Petra Lenz of Pacific Biosciences Research Center at the University of Hawaiʻi Mānoa. Dr. Lenz is also currently a rotator at the National Science Foundation, serving as Program Director for Biological Oceanography in the Directorate of Geosciences. Her talk focused on the environmental transcriptomics of a copepod model. See the full abstract and her bio here.
If you missed this very interesting talk, and the subsequent international discussion, it is now available on our YouTube channel.
If you are interested in other upcoming talks, please register here.
Starting your own transcriptomics project
If you are interested in doing similar work in transcriptomics and differential expression, we can help you get started with our resources and community tools. Once you have interesting biological results, we can feature you in a research highlight on our website or in a future webinar!
Background information worth checking out before diving into transcriptome assembly
HPC Onboarding for Biologists, a self-guided course. This is a good place to start if you are unfamiliar with clusters, clouds, or the command line. Note that the transcriptome workshop, listed below, also covers an intro to our cluster, but with less depth than this course.
-Sign in with IU username and password; see ‘modules’ for course videos.
NCGAS transcriptome assembly workshop. We will hold it again in the summer (2021), but in the meantime, feel free to look at the previous powerpoints, videos, and a tutorial with demo data for learning to assemble a transcriptome.
-See ‘More information’ for links to videos and slides.
A must-watch video on assembly strategy and what our workflow does.
A useful blog post on EviGene, the final step in our workflow that combines all the assemblies from different algorithms and kmers.
A discussion of kmer choice mentioned in our workshop.
Community tools for your project
Ready to assembly a de novo transcriptome? Our pipeline for assembling from RNAseq data without a genome is pretty popular. You can use this for individual assemblies or co-assemblies (discussed in this month’s webinar). It also includes a QC table for metrics (thanks to Juliet Wong for the suggestion), annotation support using trinotate, and DE support
For a list of recent publications using this pipeline, see our report on the workshop and workflow here
Looking for a genome-guided approach? We have that as well, but it hasn’t been fully documented, so it’s not on our Github – yet! We’re happy to share it with anyone interested – it’ll give us an excuse to document it! Email firstname.lastname@example.org if you are interested!
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. Our first one will be Tuesday, March 23, 2:00-4:00 PM EST and will be held through Discord (ncgas.help.desk, please email email@example.com for an invitation email or if you are not on our mailing list!)
One-on-one consulting & troubleshooting: email firstname.lastname@example.org