Question: Cufflinks/merge/diff tools deprecated
gravatar for aaweiner
10 weeks ago by
aaweiner0 wrote:

I've been using a HISAT2 -> Cufflinks -> Cuffmerge -> Cuffdiff -> CummeRbund pipeline to analyze some RNA-seq data. I've used many of these tools through Galaxy before but it seems that Cufflinks, Cuffmerge, and Cuffdiff are all listed as "deprecated" and I couldn't find much on this online or in pervious posts. Will this be resolved soon and are they okay to use while listed as deprecated?



rna-seq galaxy cufflinks • 307 views
ADD COMMENTlink modified 10 weeks ago by Jennifer Hillman Jackson25k • written 10 weeks ago by aaweiner0
gravatar for Jennifer Hillman Jackson
10 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:


Yes, the tools are now considered deprecated and will not be updated further. There are known issues with Tophat and Cuffdiff. More issues may come up as Galaxy is upgraded and the tools are not. CummeRbund may also be deprecated soon as there is no way to produce the needed input in Galaxy (this is one of the problems with Cuffdiff - the SQLite database for CummeRbund cannot be created -- and jobs will error if that output option is used).

Try using the new tools/methods instead. This tutorial covers the usage:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 10 weeks ago by Jennifer Hillman Jackson25k
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