Question: Top Hat deprecation--what should I use?
gravatar for sadequr.rahman
7 months ago by
sadequr.rahman10 wrote:

Dear All,

I am a novice to Galaxy and I was working through the RNA-seq tutorial.

At one stage the tutorial asks you to use TopHat but when I went to the RNAseq tools I found out that it says TopHat is now being deprecated. Should we be using RNAstar instead now? Is there a tutorial for RNAstar please? Or do you suggest I continue using TopHat gapped until I am more confident about what I am doing?

rna-seq tophat star mapping hisat2 • 273 views
ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson25k • written 7 months ago by sadequr.rahman10
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:


STAR and HISAT2 are both better choices.

HISAT2 replaces Tophat/Tophat2. STAR is used for specific reasons and uses much more resources (memory) to process data and if that tool's functions are not needed, HISAT2 is the choice.

Please see the RNA-seq Galaxy tutorials for example usage and workflows: Start with these, but review the others near the top of the list for general usage, data prep, and to learn about functions such as Dataset Collections:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson25k
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