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.