RNA-seq updated protocol

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Hi guys,
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,
Dot.

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I’m also interested in the topic.

I see from the training material GTN they use HISAT2>featureCount>limma-voon

Probably a protocol with bowtie/STAR>htseq-count>deseq2/edgeR is also used more than the old Tophat, but let’s others suggest?

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For transcript assembly, Hisat2 > StringTie is the modern equivalent of Tophat > Cufflinks.

For differential expression, it’s still hard to define one best practice, but feature-counts > DeSeq2 is generally a reasonable choice.

Tutorial here outlines this full workflow: https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/de-novo/tutorial.html

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Thanks a lot!