I was using galaxy few years ago to analyse my RNA-seq data. I wanted to use it again, for another project, however I noticed the tools I used before (tophat cufflinks) are deprecated. What is currently best pipeline to analyse RNA-seq? Could you share with me any tutorials/protocols? I know this question has been asked before, however it seems that the links are broken (“troubleshooting resources for errors or unexpected results”).
Thank you very much in advance,