RNA-seq updated protocol

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.

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?

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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