# Cuffmerge does not merge to one GTF file -- Deprecated tool: consider alternative methods

**URL:** <https://help.galaxyproject.org/t/cuffmerge-does-not-merge-to-one-gtf-file-deprecated-tool-consider-alternative-methods/6622>\
**Category:** usegalaxy.org support\
**Tags:** deprecated, tool-deprecated\
**Created:** [September 2, 2021, 10:50am UTC](https://help.galaxyproject.org/t/cuffmerge-does-not-merge-to-one-gtf-file-deprecated-tool-consider-alternative-methods/6622 "2021-09-02T10:50:54Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![benjamin\_vdh](https://avatars.discourse-cdn.com/v4/letter/b/5daacb/32.png) [@benjamin\_vdh](https://help.galaxyproject.org/u/benjamin_vdh)\
**Post date:** [September 2, 2021, 10:50am UTC](https://help.galaxyproject.org/t/cuffmerge-does-not-merge-to-one-gtf-file-deprecated-tool-consider-alternative-methods/6622/1 "2021-09-02T10:50:54Z")

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Hello,  
I have a problem with Cuffmerge and hope that someone can help me with it.

After mapping with RNA STAR I used the .bam-files (from 12 samples) to assemble transcripts with Cufflinks. With the resulting 12 gtf-files I used Cuffmerge to merge them to one .gtf-file (to use it for transcript expression analysis) - but as an output I got 12 individual .gtf-files, not one merged file… what do I do wrong?

Thanks in advance for your help.

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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:** [September 9, 2021, 3:34pm UTC](https://help.galaxyproject.org/t/cuffmerge-does-not-merge-to-one-gtf-file-deprecated-tool-consider-alternative-methods/6622/3 "2021-09-09T15:34:15Z")

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Hi @benjamin_vdh

`Cuffmerge` and all of the other Tuxedo tools are deprecated and should be avoided. The tools may not even fail, but produce odd results that are difficult to detect.

That said, for this specific case, and assuming the function is intact (it may not be) – my guess is that you are entering the inputs in a way that creates separate jobs instead of one single merged job.

Older Q&A about these tools can be found in the searches below if you are willing to tolerate/troubleshoot potential problems. Because of so many unresolved issues with deprecated tools, we can’t help troubleshoot – any functionality could be impacted (technical or scientific) the wrappers will not have any more changes. They are available for convenience reasons only and are expected to be removed from the ToolPanel entirely sometime in the future: [Searching the Galaxy](https://galaxyproject.org/search/?q=cuffmerge#gsc.tab=0&gsc.q=cuffmerge&gsc.page=1) && [Search results for 'cuffmerge' - Galaxy Community Help](https://help.galaxyproject.org/search?q=cuffmerge)

**What to do?**  **Update your analysis workflow to use currently supported tools.**

> **[Galaxy Training: Transcriptomics](https://training.galaxyproject.org/training-material/topics/transcriptomics/)**
>
> Training material for all kinds of transcriptomics analysis.