RNASeqProject

Using Galaxy to compare several bioinformatics pipelines for differential gene expression in Drosophila

Galaxy on BisonNet

https://galaxy.bucknell.edu

Tutorials

1. Galaxy
2. SARTools

Brooks et al.

Conservation of an RNA regulatory map between Drosophila and mammals https://genome.cshlp.org/content/21/2/193.full

Samples

Untreated samples:

• SRR031711 http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR031711
• SRR031714 http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR031714
• SRR031716 http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR031716

RNAi-treated samples

• SRR031718 http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR031718
• SRR031724 http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR031724
• SRR031726 http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR031726

Williams et al. 2017

Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq https://doi.org/10.1186/s12859-016-1457-z

DE Browser

DEBrowser: interactive differential expression analysis and visualization tool for count data

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore and Manuel Garber, BMC Genomics 2019 20:6.

https://doi.org/10.1186/s12864-018-5362-x

Vernia et al.

https://doi.org/10.1016/j.cmet.2014.06.010

Vangala et al.

https://doi.org/10.1016/j.cels.2018.01.002