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Oqtans Use Cases

Oqtans benefits from having a multitude of RNA-seq tools integrated into a single, overarching framework that is independent from programming languages and operating systems, provides transparent, remote access to state-of-the-art computational resources, and makes bioinformatics research reproducible. In the two following scenarios, we demonstrate how Oqtans can be harnessed for transcriptome analysis; these cases pose just two of the many possible questions that can be answered with a different combination of Oqtans tools.

GO Term Analysis of Fruit Fly Data

For this use case, we are interested in the differential expression between male and female Drosophila melanogaster fruit flies. For this purpose, we analyze data from a study of the D. melanogaster transcriptome [1]. This analysis requires three major steps: read alignment, quantification and enrichment analysis. The chosen Oqtans tools were combined in a workflow.

For more detail, please look at the galaxy page dedicated to use case I on Oqtans

Gene family expression in Arabidopsis thaliana

In the second use case, we compute and visualize fractions of unexpressed, expressed, and differentially expressed gene families. Different gene families often behave differently when comparing the expression levels of two natural accessions (strains) from the same species. In this example, we examine two strains from the model plant Arabidopsis thaliana. This example comes from the study of genomes and transcriptomes of multiple Arabidopsis strains [2] that compares the reference sequence Col-0 (Columbia) to the accession known as Can-0 (Canary Islands). The latter accession comes from a population that was isolated for a long time and shows many differences to the reference sequence. Comparing lists of differentially expressed genes among different strains of the same species leads to interesting biological insights.

For more detail, please look at the galaxy page dedicated to use case II on Oqtans

Galaxy 101 Tutorial with Arabidopsis thaliana data

In addition to these two usecases, we make available a usecase for using Galaxy (not specific to Oqtans). This example is based on Anton Nekrutenko's Galaxy 101 Tutorial and repeats these steps using data from A. thaliana. We compare the position of SNPs with the genome annotation of Chromosome 1 of the reference strain Columbia-0.

For more detail, please look at the galaxy page dedicated to Galaxy 101 example on Oqtans


[1]Daines, B., Wang, H., Wang, L., Li, Y., Han, Y., Emmert, D., Gelbart, W., Wang, X., Li, W., Gibbs, R., Chen, R. (2011). The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Res. 21(2): 315--324.
[2]Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Rätsch G, Mott R. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature. 2011 Aug 28;477(7365):419-23.
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