TopHat tool missing?

Question: TopHat tool missing?

18 months ago by

johanvn • 10 wrote:

Hi all

Is it just me or is anyone else having a hard time finding the TopHat tool? I have search for it and looked in every foler", but i cannot find it. Has it been removed or has the name changed - or am i simply blind?

rna-seq tophat hisat usegalaxy.org • 2.3k views

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modified 17 months ago by franklin_moreno • 0 • written 18 months ago by johanvn • 10

18 months ago by

Anton Nekrutenko ♦ 1.7k

Penn State

Anton Nekrutenko ♦ 1.7k wrote:

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

ADD COMMENT • link modified 18 months ago by Mo Heydarian ♦ 830 • written 18 months ago by Anton Nekrutenko ♦ 1.7k

Sorry, but I can't find the options "Report alignments tailored specifically for Cufflinks".

ADD REPLY • link written 17 months ago by vtrevino • 30

Make sure that the mapping tool used is HISAT2 (other mapping tools do not include this option). On the tool version installed at http://usegalaxy.org (Galaxy Version 2.0.5.1) these options are available as Anton describes (I just double checked).

These are nested parameters, so perhaps you need to expand the option group Spliced alignment parameters to find the setting? Once expanded, scroll down, and Cufflinks-specific output choice is near the end of that parameter block on the tool form.
If working elsewhere, maybe the HISAT tool and/or Galaxy needs to be updated to the most current version?

Thanks! Jen, Galaxy team

ADD REPLY • link modified 17 months ago • written 17 months ago by Jennifer Hillman Jackson ♦ 25k

18 months ago by

Mo Heydarian ♦ 830

United States

Mo Heydarian ♦ 830 wrote:

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

ADD COMMENT • link written 18 months ago by Mo Heydarian ♦ 830

18 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

UPDATE 06-05-20017

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

ADD COMMENT • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k

18 months ago by

franklin_moreno • 0

franklin_moreno • 0 wrote:

Hi all..

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

ADD COMMENT • link written 18 months ago by franklin_moreno • 0

Hello, Our administrator is reviewing the delays. More feedback once resolved. Meanwhile, please leave queued jobs as queued to preserve your placement. If something else needs to be done, we'll let you know. Thanks for reporting the problem! Jen, Galaxy team

ADD REPLY • link written 17 months ago by Jennifer Hillman Jackson ♦ 25k

17 months ago by

franklin_moreno • 0

franklin_moreno • 0 wrote:

Thanks a lot Jennifer! Sure I´m still waiting..

ADD COMMENT • link written 17 months ago by franklin_moreno • 0

Hi Franklin,

I also noticed that there are Trinity jobs in your history that completed but have a warning in the expanded dataset box that metadata needs to be reset. This is a standard warning for when the database had trouble setting the metadata directly. This output was used as the input custom genome for the stalled jobs.

Do this:

Delete the stalled HISAT and RNASTAR jobs
Correct the metadata on the Trinity result datasets by clicking on the provided "reset metadata" link.
Some QA or filtering will probably be needed on the raw Trinity results before the data is used as a custom reference genome. An example how-to is in the tutorial "Intro to Using Galaxy for Bioinformatics" here: https://galaxyproject.org/learn/ or you can use your own methods.
Rerun the mapping jobs using the reviewed and potentially modified assembly results from Trinity.

Highly fragmented assemblies used as custom reference genomes usually fail for resources, so the QA step is important.

Thanks! Jen, Galaxy team

ADD REPLY • link modified 17 months ago • written 17 months ago by Jennifer Hillman Jackson ♦ 25k

17 months ago by

franklin_moreno • 0

franklin_moreno • 0 wrote:

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.

ADD COMMENT • link written 17 months ago by franklin_moreno • 0

Yes, that particular tool is not available at http://usegalaxy.org. Alternatives are to use a combination of tools from the Text Manipulation and Fasta Manipulation tool groups to perform a general statistical analysis or to use this tool loaded from the Tool Shed in your own local Galaxy.

ADD REPLY • link written 17 months ago by Jennifer Hillman Jackson ♦ 25k

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