We deprecated TopHat in favor of HISAT2 - a much more efficient spliced aligner from the same group. It can be used as a drop-in replacement in your previous TopHat analyses. There are two ways is which you can perform downstream analyses:
- you can continue using CuffLinks
- you can use a new transcript assembly tool called StringTie (<- this is the recommended option)
If you choose to continue using CuffLinks, you can tell HISAT2 to output results in a Cufflinks compatible way. To do this expand Spliced alignment parameters and click Report alignments tailored specifically for Cufflinks radio button. The following image shows this part of HiSat2 interface in Galaxy:
The following paper describes HISAT: http://www.nature.com/nmeth/journal/v12/n4/full/nmeth.3317.html
This paper discusses StringTie: http://www.nature.com/nbt/journal/v33/n3/full/nbt.3122.html
An additional option for mapping RNA-seq reads is the tool RNA Star. HISAT2 and RNA Star have similar performance and accuracy on high quality libraries. RNA Star provides more robust alignments on lower quality libraries (or ones with high levels of polymorphisms) than HISAT2.
For further information on RNA Star see: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/
For further reading on HISAT2 vs. RNA Star performance see: http://www.nature.com/nmeth/journal/v14/n2/full/nmeth.4106.html
Tophat has been placed in the tool panel again if it really needs to be used for an analysis/training reason. It was always available for use when contained within and executed from an existing workflow. The tool is tagged as deprecated and will not undergo further changes.
Using HISAT or RNASTAR remain the best choices for mapping RNA-seq data as described in Anton's and Mo's replies.
Thanks! Jen, Galaxy team
Please, sb tell me... How long is a normal job going to take on HISAT? I´m runing several jobs over HISAT and RNA STAR since jun 4th, but there are no changes in the job status. Before, I ran an assembly on Trinity and it was very fast,, just some hours. Thanks a lot
Thanks Jenny! I´ve alreday solved the metadata errors. After looking at the tutorial you recommended, I notice that the tool for assessing the quality assembly is not actually among the tools (assemblystats). What other tool could I use for this purpose?
Thanks a lot.