# What file to use for Deseq2 and where to get it from

**URL:** <https://help.galaxyproject.org/t/what-file-to-use-for-deseq2-and-where-to-get-it-from/5590>\
**Category:** usegalaxy.org support\
**Tags:** gtn-tutorial, development-tools, salmon\
**Created:** [March 12, 2021, 1:40pm UTC](https://help.galaxyproject.org/t/what-file-to-use-for-deseq2-and-where-to-get-it-from/5590 "2021-03-12T13:40:04Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Ashwin\_G.k](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/ashwin_g.k/32/2228_2.png) [@Ashwin\_G.k](https://help.galaxyproject.org/u/Ashwin_G.k)\
**Post date:** [March 12, 2021, 1:40pm UTC](https://help.galaxyproject.org/t/what-file-to-use-for-deseq2-and-where-to-get-it-from/5590/1 "2021-03-12T13:40:04Z")

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Hello everyone, I wanted to use Deseq 2 and till now I used the SRA data for mapping and Quality check but I’m not able to do that for Deseq2, can anyone suggest which data to take and how to get that data in Galaxy.

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**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\
**Post date:** [March 15, 2021, 11:38am UTC](https://help.galaxyproject.org/t/what-file-to-use-for-deseq2-and-where-to-get-it-from/5590/2 "2021-03-15T11:38:40Z")

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Hi @Ashwin_G.k,  
it depends on your approach; did you mapped your reads against the genome (e.g. STAR or HISAT2) or did you perform a quasi-mapping approach (e.g. Salmon or Kallisto). I recommend you to have a look at the [transcriptomics training material](https://training.galaxyproject.org/training-material/topics/transcriptomics/).

Regards

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**Author:** ![Ashwin\_G.k](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/ashwin_g.k/32/2228_2.png) [@Ashwin\_G.k](https://help.galaxyproject.org/u/Ashwin_G.k)\
**Post date:** [March 16, 2021, 12:26pm UTC](https://help.galaxyproject.org/t/what-file-to-use-for-deseq2-and-where-to-get-it-from/5590/3 "2021-03-16T12:26:02Z")

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Hello Sir, I mapped my reads against the genome using Rna sta, so how do i proceed further and also could you enlighten me if i’m using quasi approach as well?.

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**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\
**Post date:** [March 19, 2021, 3:34pm UTC](https://help.galaxyproject.org/t/what-file-to-use-for-deseq2-and-where-to-get-it-from/5590/4 "2021-03-19T15:34:41Z")

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Hi @Ashwin_G.k,  
I recommend you to have a look at these two histories; they describe the whole workflow for mapping the reads by using both RNA STAR and SALMON.

- [Differential expression with SALMON](https://usegalaxy.eu/u/gallardoalba/h/de-br-salmon)
- [Differential expression with RNA STAR](https://usegalaxy.eu/u/gallardoalba/h/plant-reference-based-rna-seq)

Let me know if you have any doubt.

Regards