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

To Galaxy Team,
I am writing to ask your kind help/suggestion regarding to the use of galaxy (https://usegalaxy.org) to analyze RNA-seq data.

First, when I was trying to use “Tophat” and “cufflinks” to analyze my RNA-seq data, I noticed that these functions were labeled with “deprecated”. Does “deprecated” mean that “Tophat” and “cufflinks” are no longer to be good methods to analyze RNA-seq data? Are the results obtained from “Tophat” reliable? If not, what methods in Galaxy do you suggest us to use?

Second, I found that HISAT2 can also be used for transcriptome analysis. However, there is no reference genome for Arabidopsis thaliana. Can we use the downloaded reference genome of Arabidopsis for analysis? And what format does a reference genome require?

Your kind and timely help would be highly appreciated. I look forward to your reply at your earliest convenience.

Best wishes!
Yaoguang Yu

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

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.

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):

@jennaj, Hi I am using cufflinks in galaxy Europe for RNA seq analysis but I couldn’t find any reference annotation guide " B73 RefGen_v4" of maize, I tried to get from the web but I couldn’t, the built-in reference genome is present in tophat but not in cufflinks. How can I get B73 RefGen_v4" reference genome assembly of maize into cufflinks for expression analysis?