Effective Tuesday July 21 on lonepeak
posted 7 July 2020
Access permissions to /scratch/local will be set such that users will no longer be able to created directories in the top level /scratch/local directory. Instead, as part of the slurm job prolog (before the job is started), a job level directory, /scratch/local/$USER/$SLURM_JOB_ID , will be created. After the end of the job, in the slurm job epilog, this job level directory will be removed.
Once we confirm there are no issues on lonepeak, we will make the same change on the other clusters (kingspeak, notchpeak, ash and redwood)
- Intro to Open OnDemand: Tue, July 7th, 1-3 pm
- Intro to R: Thur, July 9th, 1-3 pm
- Intro to Parallel Computing: Tue, July 14th, 1-2 pm
CHPC DOWNTIME: 6/9/2020 at 8am - mysql.chpc.utah.edu and windows servers (Narwhal, Beehive) and the community MySQL server
Posted May 27th, 2020
Posted May 14th, 2020
Posted May 5th, 2020
Posted May 1st, 2020
Posted April 24th, 2020
Posted: March 31st, 2020
Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia)
By Carson Holt, Michael Campbell, David A. Keays, Nathaniel Edelman, Aurélie Kapusta, Emily Maclary, Eric T. Domyan, Alexander Suh, Wesley C. Warren, Mark Yandell, M. Thomas P. Gilbert, and Michael D. Shapiro, Shapiro Lab, Department of Biology
Intensive selective breeding of the domestic rock pigeon (Columba livia) has resulted in more than 350 breeds that display extreme differences in morphology and behavior (Levi 1986; Domyan and Shapiro 2017). The large phenotypic differences among different breeds make them a useful model for studying the genetic basis of radical phenotypic changes, which are more typically found among different species rather than within a single species.
In genetic and genomic studies of C. livia, linkage analysis is important for identifying genotypes associated with specific phenotypic traits of interest (Domyan and Shapiro 2017); however, short scaffold sizes in the Cliv_1.0 draft reference assembly (Shapiro et al. 2013) hinder computationally-based comparative analyses. Short scaffolds also make it more difficult to identify structural changes, such as large insertions or deletions, that are responsible for traits of interest (Domyan et al. 2014; Kronenberg et al. 2015).
Here we present the Cliv_2.1 reference assembly and an updated gene annotation set. The new assembly greatly improves scaffold length over the previous draft reference assembly, and updated gene annotations show improved concordance with both transcriptome and protein homology evidence.
Read the full article as it appears in G3.