# Trinity align reads and estimate abundance Fatal Error **URL:** \ **Category:** usegalaxy.org support\ **Tags:** assembly, troubleshooting, salmon\ **Created:** [June 22, 2020, 8:37pm UTC](https://help.galaxyproject.org/t/trinity-align-reads-and-estimate-abundance-fatal-error/3961 "2020-06-22T20:37:40Z")\ **Posts on this page:** 1\ **Showing post:** 6
**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:** [June 23, 2020, 2:33am UTC](https://help.galaxyproject.org/t/trinity-align-reads-and-estimate-abundance-fatal-error/3961/6 "2020-06-23T02:33:59Z")
If your reads were not quality trimmed before assembly, then you should do that first. Resources about the `Trinity` pipeline, include assembly statistics tools: > [@What to do with trinity output files](https://help.galaxyproject.org/t/what-to-do-with-trinity-output-files/2497/2): > > Welcome @Priya_GNDU! Tool: Build expression matrix for a de novo assembly of RNA-Seq data by Trinity Resources for generating/working with Trinity assemblies: Author’s Wiki, includes links to tutorials/resources: [Home · trinityrnaseq/trinityrnaseq Wiki · GitHub](https://github.com/trinityrnaseq/trinityrnaseq/wiki)[Accessing Trinity on Publicly Available Compute Resources · trinityrnaseq/trinityrnaseq Wiki · GitHub](https://github.com/trinityrnaseq/trinityrnaseq/wiki/Accessing-Trinity-on-Publicly-Available-Compute-Resources)[Home · trinityrnaseq/GalaxyTrinityProtocol Wiki · GitHub](https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki) The Trinity command-line tools are wrapped for Galaxy. Help is on eac… > [@What are the RNA-seq data processing steps in Galaxy according to de novo approach?](https://help.galaxyproject.org/t/what-are-the-rna-seq-data-processing-steps-in-galaxy-according-to-de-novo-approach/3943/2): > > Hi @f_kurt Please see this prior Q&A, it covers most of what you are asking about. It is worth reviewing first: [What to do with trinity output files](https://help.galaxyproject.org/t/what-to-do-with-trinity-output-files/2497) For tools that appear to be missing, it could be that the Galaxy server you are working at does not have them installed. Or, the tool panel search is not finding them for some reason (search term typo?). You can also directly check. Trimmomatic is often under the tool group “FASTQ Quality Control”. And yes, performing QA is probably a good idea… That said, I still think this could be a server-side issue. These tools were designed to work with data that isn’t “perfect”. You could also try alternative options than `RSEM` – `Salmon` or `Kalisto` as others needed to do (see the ticket that the `Trinity` authors wrote back on [Trinity transcript\_abundance.pl error using RSEM · Issue #305 · trinityrnaseq/trinityrnaseq · GitHub](https://github.com/trinityrnaseq/trinityrnaseq/issues/305)). But if this is an actual cluster issue, those wouldn’t work either. In testing today, many tools that run on the same cluster as this one all failed. Our administrator is working on it. --- _[View the full topic](https://help.galaxyproject.org/t/trinity-align-reads-and-estimate-abundance-fatal-error/3961)._