# RNA seq analysis: deprecated tools, updated tools, learning resources

**URL:** <https://help.galaxyproject.org/t/rna-seq-analysis-deprecated-tools-updated-tools-learning-resources/159>\
**Category:** usegalaxy.org support\
**Tags:** gtn-tutorial, transcriptomics\
**Created:** [December 8, 2018, 2:34am UTC](https://help.galaxyproject.org/t/rna-seq-analysis-deprecated-tools-updated-tools-learning-resources/159 "2018-12-08T02:34:03Z")\
**Posts on this page:** 1\
**Showing post:** 2

<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:** [December 10, 2018, 7:23pm UTC](https://help.galaxyproject.org/t/rna-seq-analysis-deprecated-tools-updated-tools-learning-resources/159/2 "2018-12-10T19:23:51Z")

</div>

Hello,

Yes, both **Tophat** and **Cufflinks** are deprecated in favor of more current tools/methods for RNA-seq analysis.

> [@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.

The _TAIR10_ genome is indexed for **HISAT2** at Galaxy EU [https://usegalaxy.eu](https://usegalaxy.eu).

We are working to standardize the genomes and indexes between all usegalaxy.\* servers but this is still a work in progress. If you want to work with _Arabidopsis_ at Galaxy Main [https://usegalaxy.org](https://usegalaxy.org) right now, you’ll need to use it as a `Custom Reference Genome` with many tools.

> [@Troubleshooting resources for errors or unexpected results](https://help.galaxyproject.org/t/troubleshooting-resources-for-errors-or-unexpected-results/42/1):
>
> - [All Galaxy Support FAQs](https://galaxyproject.org/support/)

Start with the first if you choose to use a Custom Genome. The second explains how to make sure any reference annotation that you incorporate is a match for the genome and indexes used in the same analysis (Custom or Built-in):

- [Preparing and using a Custom Reference Genome or Build](https://galaxyproject.org/learn/custom-genomes/)
- [Mismatched Chromosome identifiers (and how to avoid them)](https://galaxyproject.org/support/chrom-identifiers/)

---

_[View the full topic](https://help.galaxyproject.org/t/rna-seq-analysis-deprecated-tools-updated-tools-learning-resources/159)._