RNA seq analysis: deprecated tools, updated tools, learning resources

[jennaj]

Hello,

Yes, both Tophat and Cufflinks are deprecated in favor of more current tools/methods for RNA-seq analysis.

@jennaj

• Galaxy Training Network Tutorials: Some GTN tutorials are appropriate for Galaxy Main and some are not. Where you can run each is noted per tutorial – click on the Galaxy instances gear icon to review the Public Galaxy server choices. If a tutorial is supported by a pre-configured Galaxy Docker training image, instructions for how to get it will be listed below the tutorial listings, per category.

The TAIR10 genome is indexed for HISAT2 at Galaxy EU https://usegalaxy.eu.

We are working to standardize the genomes and indexes between all usegalaxy.* servers but this is still a work in progress. If you want to work with Arabidopsis at Galaxy Main https://usegalaxy.org right now, you’ll need to use it as a Custom Reference Genome with many tools.

@jennaj

• All Galaxy Support FAQs

Start with the first if you choose to use a Custom Genome. The second explains how to make sure any reference annotation that you incorporate is a match for the genome and indexes used in the same analysis (Custom or Built-in):

• Preparing and using a Custom Reference Genome or Build
• Mismatched Chromosome identifiers (and how to avoid them)