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Genetics and Genomics Commons™

Open Access. Powered by Scholars. Published by Universities.®

Genomics

2018

Metagenomics

Articles 1 - 3 of 3

Full-Text Articles in Genetics and Genomics

Fastqc Analysis & Hisat Alignments Using Cyverse (Part 2), Ray A. Enke Oct 2018

Fastqc Analysis & Hisat Alignments Using Cyverse (Part 2), Ray A. Enke

Ray Enke Ph.D.

Part 2 of this in class exercise uses CyVerse Discovery Environment (DE) for the following:
  • view the output files of FastQC analysis
  • create custom data tracks from HISAT alignment files for visualization in the UCSC Genome Browser

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Fastqc Analysis & Hisat Alignments Using Cyverse (Part 1), Ray A. Enke Oct 2018

Fastqc Analysis & Hisat Alignments Using Cyverse (Part 1), Ray A. Enke

Ray Enke Ph.D.

This in class exercise demonstrates the basic features of the CyVerse Discovery Environment (DE) cyberinfrastructure and also provides a tutorial for setting up FastQC analysis of next generation sequencing reads as well as HISAT alignment of eukaryotic RNA-seq FASTQ files.

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Determining Bioindicators For Coastal Tidal Marsh Health Using The Food Web Of Larvae Of The Greenhead Horse Fly (Tabanus Nigrovittatus), Devika Rajeev Bhalerao Jan 2018

Determining Bioindicators For Coastal Tidal Marsh Health Using The Food Web Of Larvae Of The Greenhead Horse Fly (Tabanus Nigrovittatus), Devika Rajeev Bhalerao

LSU Master's Theses

The greenhead horse fly Tabanus nigrovittatus Macquart is native to coastal marshlands from Texas to Nova Scotia. The larvae are apex invertebrate predators and their development is dependent on the food web in the soil. Surveillance of T. nigrovittatus after the 2010 Deepwater Horizon oil spill in the Gulf of Mexico showed population crashes of adults in the coastal marshes of East Louisiana near places where oil made landfall, but not in West Louisiana where the oil did not reach. Sediment collection in 2011 from West and East Louisiana revealed larval population crashes in the Eastern coastal region. We hypothesized …

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