# Data paused and keep getting error: Tophat RNA data -- Tophat/Tophat2 Deprecated, use HISAT2

**URL:** <https://help.galaxyproject.org/t/data-paused-and-keep-getting-error-tophat-rna-data-tophat-tophat2-deprecated-use-hisat2/3609>\
**Category:** Uncategorized\
**Tags:** mapping, transcriptomics, tool-deprecated\
**Created:** [May 8, 2020, 11:59am UTC](https://help.galaxyproject.org/t/data-paused-and-keep-getting-error-tophat-rna-data-tophat-tophat2-deprecated-use-hisat2/3609 "2020-05-08T11:59:14Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![ajisa\_ali](https://avatars.discourse-cdn.com/v4/letter/a/a3d4f5/32.png) [@ajisa\_ali](https://help.galaxyproject.org/u/ajisa_ali)\
**Post date:** [May 8, 2020, 11:59am UTC](https://help.galaxyproject.org/t/data-paused-and-keep-getting-error-tophat-rna-data-tophat-tophat2-deprecated-use-hisat2/3609/1 "2020-05-08T11:59:14Z")

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Hello,

I have uploaded some files from ncbi and trying to do multiple analysis using tophat RNA seq. It keep going into pause and then it comes up with error. can someone help please?

Thanks

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<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [May 8, 2020, 3:42pm UTC](https://help.galaxyproject.org/t/data-paused-and-keep-getting-error-tophat-rna-data-tophat-tophat2-deprecated-use-hisat2/3609/2 "2020-05-08T15:42:07Z")

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Hello @ajisa_ali

The tools `Tophat` and `Tophat2` have been deprecated for many years. `HISAT2` is the replacement.

To learn more about current Transcriptomics methods and tools, please see:

> [@Troubleshooting resources for errors or unexpected results](https://help.galaxyproject.org/t/troubleshooting-resources-for-errors-or-unexpected-results/42/1):
>
> [Galaxy Training Network Tutorials](https://galaxyproject.github.io/training-material/): Some [GTN](https://galaxyproject.org/teach/gtn/) tutorials are appropriate for [Galaxy Main](https://usegalaxy.org) and some are not. Where you can run each is noted per tutorial – click on the _Galaxy instances_ gear icon ![galaxyserversGTN](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/1X/1287f50cfcdaa1aad750fe323f96995260ac4947.png) to review the [Public Galaxy](https://galaxyproject.org/use/) server choices. If a tutorial is supported by a pre-configured [Galaxy Docker](https://hub.docker.com/r/bgruening/galaxy-stable/) training image, instructions for how to get it will be listed below the tutorial listings, per category.

Thanks!