The post describes how to allow Globus transfers between IU endpoints and an external hard drive.
... Read more »NCGAS Service Changes
Changes to NCGAS services – starting December 31, 2021
... Read more »
Introduction to Illumina Sequencing
NCGAS is teaching a course in genomics, called GEMS: WORKFLOWS IN GENOMICS. GEMS is Genomics and Eco-evolution of Multi-scale Symbioses. Included in all this are short introductions to Illumina and Nanopore sequencing. I thought I would give these to you as blogs, this one on Illumina and another to come on Nanopore, and eventually one on PacBio. Note that we recently posted a blog on next generation sequencing, i.e. long read sequencing methods. That has a different flavor from what I’m doing here.
... Read more »Installing Genomics Software with Biocontainers
How to get easy-to-install software from the Biocontainer community project!
... Read more »Circle-sequencing RNA
We hosted Jean-Francois Gout of Mississippi State University this month. Jean-Francois did his post-doc work with the Lynch Lab at Indiana University and then Arizona State University (when the Lynch Lab relocated). He spoke about RNA transcription error and how to detect and study them using novel circle-sequencing of the RNA to produce multiple copies… Read more »
Tunneling a Jupyter Notebook from an HPC
Jupyter Notebook Tunneling is a convenient trick to have in your back pocket, especially when the resources on your personal computer are limiting your progress. Tunneling allows you to run your notebook from a remote host such that your processes utilize the resources available on your host, rather than your personal computer. In this brief… Read more »
Differential Expression Resources
A one-stop list of our most popular differential expression resources for background, tutorials, and code to do your own project.
... Read more »A Quick Intro to Singularity Containers
What is Singularity? A Singularity container is used to encapsulate all required software and dependencies for a workflow. This is extremely useful when trying to execute a particular workflow on different systems. Containers make compiling software on different compute platforms easy and effortless. The best part is you don’t need admin privileges with Singularity if… Read more »
An up-date on next generation sequencing and scaffolding, 04/2021
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 »