Tag: CyVerse

UCSC Genome Browser Custom Track Blank

UCSC Genome Browser Custom Track Blank 0 Hello, I have a bigwig (.bw) file which I can properly view on IGV. IGV makes it very difficult to edit the figure nicely so I am trying to view it in the UCSC genome browser. I uploaded my data to cyverse and…

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Extracting Functional Traits from Large Volumes of Field Phenomics Data

Authors: Emmanuel Miguel Gonzalez1* (emmanuelgonzalez@arizona.edu), Ariyan Zarei1, Jeffrey Demieville1, Nimet Beyza Bozdag1, Seungho Lee1, Sarthak Bawal1, Jordan Edward Pettiford1, Yuguo Xiao2, Indrajit Kumar2, Maxwell Braud2, Eric Lyons1, Duke Pauli1, and Andrea Eveland2 Institutions: 1University of Arizona; and 2Donald Danforth Plant Science Center URLs: Goals Use the University of Arizona‚Äôs Field…

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How do you download from CyVerse using FTP or wget?

2 hours ago O.rka ▴ 650 I’m trying to download from the following URL: datacommons.cyverse.org/browse/iplant/home/shared/imicrobe/projects/277/samples/6131/S0250.fa.gz I have 39 other samples I need to download and don’t really want to click them individually. All of the resources I’ve seen to download in bulk from the command line are way different than…

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Suggestions for Alternate Assembly Resources to Trinity

Suggestions for Alternate Assembly Resources to Trinity 0 As far as I can tell, Galaxy no longer seems to support Trinity as an assembler – or at least, I have not been able to assemble any read data using Trinity for the past several months. Initially, I had had success…

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BioViz Connect: Web application linking CyVerse science gateway resources to genomic visualization in the Integrated Genome Browser

Abstract Genomics researchers do better work when they can interactively explore and visualize data. However, due to the vast size of experimental datasets, researchers are increasingly using powerful, cloud-based systems to process and analyze data. These remote systems, called science gateways, offer user-friendly, Web-based access to high performance computing and…

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