# Differentially expressed genes **URL:** \ **Category:** Uncategorized\ **Tags:** gtn-tutorial, transcriptomics, edger, salmon\ **Created:** [January 10, 2021, 11:24am UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167 "2021-01-10T11:24:15Z")\ **Posts on this page:** 15\ **Page:** 1
**Author:** ![humaira](https://avatars.discourse-cdn.com/v4/letter/h/278dde/32.png) [@humaira](https://help.galaxyproject.org/u/humaira)\ **Post date:** [January 10, 2021, 11:24am UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167/1 "2021-01-10T11:24:15Z")
Hi, I have two assembled fasta files, one for control and second for disease condition. I need to fine differentially expressed genes in both of them. Plz guide me how to perform this type of analysis. Regards ---
**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:** [January 10, 2021, 2:17pm UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167/2 "2021-01-10T14:17:45Z")
Hi @humaira, it depends on the goal of your analysis and the type of data you have. When you talk about assembled fasta files, you mean assembled transcriptomes generated by RNA-seq? Regards ---
**Author:** ![amir](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/amir/32/539_2.png) [@amir](https://help.galaxyproject.org/u/amir)\ **Post date:** [January 12, 2021, 8:03am UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167/3 "2021-01-12T08:03:31Z")
You have two Fasta or FASTQ files ? FASTA are for references. I assume you have 2 FASTQ files between two conditions. If this is true, you should align it with HISAT2 then Featurecount for quantification and Use deseq2 or edgeR for DEG. Other tools are useful too. Best ---
**Author:** ![humaira](https://avatars.discourse-cdn.com/v4/letter/h/278dde/32.png) [@humaira](https://help.galaxyproject.org/u/humaira)\ **Post date:** [May 27, 2021, 3:15pm UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167/4 "2021-05-27T15:15:53Z")
I have two fasta files. one for normal and second for diseased condition. ---
**Author:** ![amir](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/amir/32/539_2.png) [@amir](https://help.galaxyproject.org/u/amir)\ **Post date:** [May 27, 2021, 11:17pm UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167/5 "2021-05-27T23:17:59Z")
how many repeats do you have for each condition ? Best ---
**Author:** ![humaira](https://avatars.discourse-cdn.com/v4/letter/h/278dde/32.png) [@humaira](https://help.galaxyproject.org/u/humaira)\ **Post date:** [May 28, 2021, 11:00am UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167/6 "2021-05-28T11:00:58Z")
AOA. 133,900 reads for normal and 132,900 for diseased. Regards. ---
**Author:** ![amir](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/amir/32/539_2.png) [@amir](https://help.galaxyproject.org/u/amir)\ **Post date:** [May 28, 2021, 5:27pm UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167/7 "2021-05-28T17:27:39Z")
you are telling the number of your reads. i meant the number of your datasets You can use your fastas as reference genome not your main samples as i think i told you before. i assume you build your reference genome. Whats your analysis about? is it in homo sapiens fields or else ?! ---
**Author:** ![humaira](https://avatars.discourse-cdn.com/v4/letter/h/278dde/32.png) [@humaira](https://help.galaxyproject.org/u/humaira)\ **Post date:** [May 28, 2021, 6:43pm UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167/8 "2021-05-28T18:43:50Z")
I am working on transcriptome analysis of plant and no reference genome exists for this plant. ---
**Author:** ![humaira](https://avatars.discourse-cdn.com/v4/letter/h/278dde/32.png) [@humaira](https://help.galaxyproject.org/u/humaira)\ **Post date:** [June 12, 2021, 12:18pm UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167/9 "2021-06-12T12:18:18Z")
yes assembled transcriptomes generated by RNA-seq. ---
**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:** [June 14, 2021, 6:42pm UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167/10 "2021-06-14T18:42:28Z")
Hi @humaira, you can use Salmon Quant for performing the differential expression analysis. I recommend you to have a look at this tutorial: [Quantification of gene expression: Salmon](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html#quantification-of-gene-expression-salmon). Regards ---
**Author:** ![humaira](https://avatars.discourse-cdn.com/v4/letter/h/278dde/32.png) [@humaira](https://help.galaxyproject.org/u/humaira)\ **Post date:** [June 17, 2021, 12:27pm UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167/11 "2021-06-17T12:27:17Z")
Hi. Thx. now i need to separate differentially expressed transcripts from both fasta files. Guide me plz. regards ---
**Author:** ![jaredbernard](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jaredbernard/32/2595_2.png) [@jaredbernard](https://help.galaxyproject.org/u/jaredbernard)\ **Post date:** [June 17, 2021, 7:01pm UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167/12 "2021-06-17T19:01:46Z")
Here is a very useful tutorial for [assembly and differential expression of de novo transcriptomes](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/full-de-novo/tutorial.html#introduction). It should walk you through the whole process. 🙂 ---
**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 30, 2021, 10:12pm UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167/13 "2021-06-30T22:12:35Z")
9 posts were split to a new topic: [Troubleshooting problems with DESeq2](https://help.galaxyproject.org/t/troubleshooting-problems-with-deseq2/6290) ---
**Author:** ![Anand\_Mishra](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/anand_mishra/32/2039_2.png) [@Anand\_Mishra](https://help.galaxyproject.org/u/Anand_Mishra)\ **Post date:** [November 3, 2022, 2:52pm UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167/14 "2022-11-03T14:52:16Z")
> [@amir](#): > > edgeR for DEG Dear Amir this deseq2 or edge R is available on galaxy ---
**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:** [November 11, 2022, 12:02am UTC](https://help.galaxyproject.org/t/differentially-expressed-genes/5167/15 "2022-11-11T00:02:27Z")