# Tophat not working??? - Deprecated tool, use HISAT2 instead

**URL:** <https://help.galaxyproject.org/t/tophat-not-working-deprecated-tool-use-hisat2-instead/2256>\
**Category:** Uncategorized\
**Tags:** troubleshooting, mapping, tool-deprecated\
**Created:** [October 9, 2019, 2:07am UTC](https://help.galaxyproject.org/t/tophat-not-working-deprecated-tool-use-hisat2-instead/2256 "2019-10-09T02:07:27Z")\
**Posts on this page:** 1\
**Showing post:** 7

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**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:** [February 29, 2020, 1:44am UTC](https://help.galaxyproject.org/t/tophat-not-working-deprecated-tool-use-hisat2-instead/2256/7 "2020-02-29T01:44:02Z")

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Tophat has been deprecated for many years now. It is not maintained anymore and could present with issues at any time. We were able to get a workaround before, but that may no longer be possible, or if fixed, it won’t be soon.

Everyone needs to migrate away from using Tophat. HISAT2 is the replacement.

Prior Q&A that covers alternatives:

> [@Tophat error for paired data analysis (deprecated tool)](https://help.galaxyproject.org/t/tophat-error-for-paired-data-analysis-deprecated-tool/1108):
>
> I am new user and i am doing tophat for paired data but it gives error wihle i execute it Please help me error An error occurred with this dataset: Settings: Output files: “genome.\*.bt2” Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default

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_[View the full topic](https://help.galaxyproject.org/t/tophat-not-working-deprecated-tool-use-hisat2-instead/2256)._