# Getting errors for Salmon

**URL:** <https://help.galaxyproject.org/t/getting-errors-for-salmon/10918>\
**Category:** usegalaxy.org.au support\
**Tags:** transcriptomics, salmon\
**Created:** [October 10, 2023, 4:05am UTC](https://help.galaxyproject.org/t/getting-errors-for-salmon/10918 "2023-10-10T04:05:26Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![rachel.lee](https://avatars.discourse-cdn.com/v4/letter/r/df788c/32.png) [@rachel.lee](https://help.galaxyproject.org/u/rachel.lee)\
**Post date:** [October 10, 2023, 4:05am UTC](https://help.galaxyproject.org/t/getting-errors-for-salmon/10918/1 "2023-10-10T04:05:26Z")

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Hi there, I’ve been trying to use Salmon for the past few times and every time it comes up with the error “cannot find ‘ext’”. Not quite sure what went wrong. My input was the transcript fasta file (interleaved paired end) and reference genome fasta file.

 ![Screenshot 2023-10-10 140312](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/b/b026acc03db7e1d74b76ffd183c2997d1e5b5e08.png)  
 ![Screenshot 2023-10-10 140257](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/3/31267c0dcb5558eda734e6d4698692cb11c1a681.png)

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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:** [October 10, 2023, 7:25pm UTC](https://help.galaxyproject.org/t/getting-errors-for-salmon/10918/2 "2023-10-10T19:25:58Z")

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Hi @rachel.lee

This tool expects four primary inputs:

1. Post-QA Reads, can be paired end
2. transcriptome fasta
3. genome fasta (optional)
4. File containing a mapping of transcripts to genes (optional). Important for gene-level differential expression purposes.

How the transcripts are present in step 4 should contain identifiers that exactly match the **\>** lines in the transcript fasta file. Transcript identifiers in the first column, gene identifiers in the second column, and the data is separated by a tab.

Use **NormalizeFasta** if you need to remove fasta description content. If you need to do more manipulations to get those to all match up so **Salmon** can understand, please see [Data Manipulation Olympics](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html)

If you still need to do read QA, please see [Search GTN Materials](https://training.galaxyproject.org/training-material/search2?query=quality) (query=quality)

Please give that a review and you’ll likely find the problem. But if you need more help, would you please share more about the error? How the job was set up and the content of the files is all on the Job Information view and is usually enough. That is a good summary place for you to review as well when checking the items above.

> [@Getting Data into Galaxy](https://help.galaxyproject.org/t/getting-data-into-galaxy/10868/1):
>
> Any persistent problems can be reported in a new question for community help. Be sure to provide enough context so others can review the situation _exactly_ and quickly offer advice.
> 
> Consider [Sharing your History](https://training.galaxyproject.org/training-material/faqs/galaxy/histories_sharing.html) or posting content from the Job Information ℹ view as described in [Troubleshooting errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html).

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<div class="post-metadata">

**Author:** ![rachel.lee](https://avatars.discourse-cdn.com/v4/letter/r/df788c/32.png) [@rachel.lee](https://help.galaxyproject.org/u/rachel.lee)\
**Post date:** [October 18, 2023, 5:35am UTC](https://help.galaxyproject.org/t/getting-errors-for-salmon/10918/3 "2023-10-18T05:35:24Z")

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Thank you for your reply! Figured that the PE interleaved files did not work with Salmon for some reason. It’s working now with paired-end files.

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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:** [October 18, 2023, 4:50pm UTC](https://help.galaxyproject.org/t/getting-errors-for-salmon/10918/4 "2023-10-18T16:50:13Z")

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> [@rachel.lee](#):
>
> Figured that the PE interleaved files did not work with Salmon for some reason. It’s working now with paired-end files.

Thanks for posting that back @rachel.lee. I’ve seen that before but only at certain servers. Sounds like the AU server doesn’t support that option (yet). Glad you found another way!