A tool is marked deprecated, should I use it?

Question: A tool is marked deprecated, should I use it?

7 months ago by

Hi, im following a guide about how to analyse RNAseq data to do differential expression analysis. However one of the tools in the guide, TopHat, is deprecated. What does that mean? Analyses seem to never complete, stays in a queue. Best Theodor

rna-seq queue tophat tutorials hisat2 • 338 views

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modified 7 months ago by jevanveen • 10 • written 7 months ago by theodorcrispin • 0

7 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I see that your Tophat jobs finished successfully. The queue was probably just busy. https://galaxyproject.org/support/#datasets-and-histories

It would be better to use the newest tutorials and avoid older deprecated tools/methods. HISAT2 has replaced both Tophat and Tophat2. Deprecated tools may fail with a certain usage, or fail always. Older versions of a tool might do the same. Updated tool versions can include bug fixes and the like - so it is best to use the most current version unless there is a compelling reason to try to use the older one.

Galaxy tutorials: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team

ADD COMMENT • link written 7 months ago by Jennifer Hillman Jackson ♦ 25k

7 months ago by

jevanveen • 10

jevanveen • 10 wrote:

TopHat has been largely replaced by newer algorithms. Is there a reason you must use TopHat? If not, it's better to proceed with a pipeline using Hisat2 or Star for alignment dependent fragment counting or Kallisto or Salmon for alignment independent fragment counting. I've used Star followed by DEseq2 on Galaxy for DE analysis with good results as well as Salmon followed by DEseq2 also with good results.

Here is a guide for using either Star or Salmon to generate count matrices

https://www.bioconductor.org/help/workflows/rnaseqGene/

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