Journal

Genetics

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

JoVE Journal
Genetics

This content is Free Access.

JoVE Journal Genetics

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

DOI:

10.3791/55009-v

•

10:41 min

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May 09, 2017

•

Blake L. Joyce², Asher K. Haug-Baltzell, Jonathan P. Hulvey, Fiona McCarthy, Upendra Kumar Devisetty⁶, Eric Lyons^2,3

¹BIO5 Institute,University of Arizona, ²The School of Plant Sciences,University of Arizona, ³Genetics GIDP,University of Arizona, ⁴Biology Department,University of Massachusetts Amherst, ⁵School of Animal and Comparative Biomedical Sciences,University of Arizona, ⁶CyVerse,University of Arizona

Chapters

00:05Title
01:03Set Up the Project, Upload Raw Sequencing Reads, and Assess Reads Using FastQC
03:31Trim and Quality Filter Raw Reads to Yield High Quality Sequence
04:32De Novo Transcriptome Assembly Using Trinity in Atmosphere
06:42Pairwise Differential Expression Using DESeq2 in the DE
07:38Results: FastQC and rnaQUAST Reports
09:24Conclusion

Summary

Automatic Translation

This protocol outlines a comparative de novo transcriptome assembly and annotation workflow for novice bioinformaticians. The workflow is available for free entirely through CyVerse and connected by the Data Store. Command line and graphical user interfaces are used, but all code needed is available to copy and paste.

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