Our last blog on third generation sequencing is still mostly relevant and current (here), so this post is an update where improvements are noted. The methods have matured a lot. The players are still largely the same: PacBio, Nanopore, Bionano and Hi-C. 10x has dropped out of the genomics field to focus almost exclusively on… Read more »
SLURM’S UP: A Guide to Riding the Slurm Wave
On April 12, 2021, Carbonate is transitioning to the Slurm workload manager. We compiled the most essential information to work with SLURM, including information on converting your job script from Torque.
... Read more »Transcriptomics Research and Resources
We featured Dr. Petra Lenz in our first webinar, and share tools to get you started doing similar work.
... Read more »An Update to RNA-seq Technology
Since our first transcriptomics workshop in 2018, many cutting-edge RNA sequencing technologies have become more popular. Some of these methods, like Iso-Seq, have made their way into non-medical fields. Direct and single-cell RNA sequencing methods, on the other hand, are used almost exclusively in cancer biology, biomarker discovery, and neurobiology.
... Read more »A Beginner’s Guide to the SRA
The NCGAS team finds that many users unfamiliar with SRA-Toolkit or the command line struggle with configuring the program or parsing its multiple commands and options. Here, I aim to condense and distill this information so that a beginner can use the SRA to their heart’s content!
... Read more »Finding protein homologs at NCBI and making a phylogenetic tree
This blog is brought to you by NCGAS undergraduate intern Christina Campbell and is inspired by the curiosity of former NCGAS Co-PI Craig Stewart (who is now enjoying well-earned retirement). This is part of a multi-part series on exploring questions about epigenetics in beetles. Follow along as we determine which species have methylation enzymes, how these patterns are organized on the species tree of beetles, and how you can explore possible patterns of methylation – entirely with bioinformatics!
... Read more »Platypus-inspired scaffold length histograms
Visualizing the distribution of scaffold size in an assembly is a nice complement to basic summary statistics. In this blog post, I’ll describe how to plot a histogram of scaffold lengths, using the new mOrnAna1 platypus assembly as an example.
... Read more »Setting up Volumes on Jetstream
Adding volumes to your Jetstream virtual machine
... Read more »Celebrating what we can about 2020
2020 was a rough year for many reasons, but there are still things to be excited about – here are the staff picks of interesting or exciting news in 2020!
... Read more »NCGAS Galaxy Changes
Updates to our Galaxy support
... Read more »