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Trouble getting Cufflinks to run

I downloaded cufflinks but I can't seem to get it to work. The install instructions seem a bit out of date. I downloaded version 2.2 earlier and I'm having trouble getting the test_data to work. When I enter the command all I am getting is a solid grey box. Doesn't it look like it is running anything?

I think with the new version sams tool and eigen are already in there? I also don't have an option to configure cufflinks. (http://cole-trapnell-lab.github.io/cufflinks/getting_started/) I tried adding them into the path and I have the same gray box issue?

I'm running 

./cufflinks test_data.sam

Any help would be great! Thanks

rna-seq assembly
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written by williamsbrian5064 williamsbrian5064

The install instructions seem a bit out of date

Yes, 'Cufflinks' has been retired and is no longer supported. You should switch to using HISAT2 and StringTie, which perform the same functions as TopHat2/Cufflinks.

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written by Kevin Blighe Kevin Blighe

That is what I have heard. I have had success with HISAT2 and StringTie but I am wonder what to do with the data afterwards? I want to be able to do expression analysis

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written by williamsbrian5064 williamsbrian5064

Have you checked the Nature Protocols published manuscript? - https://www.nature.com/articles/nprot.2016.095

If it's just expression over already-identified genes (coding and non-coding), then you could just save yourself a lot of time and use something like Kallisto or Salmon, followed by EdgeR or DESeq2. I would only ever use HISAT2/StringTie if I was interested in finding novel splice isoforms in existing genes or new genes outright.

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written by Kevin Blighe Kevin Blighe

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