# Problems regarding file upload in DeSeq2 **URL:** \ **Category:** usegalaxy.org support\ **Tags:** tool-help, deseq2\ **Created:** [April 12, 2025, 11:04am UTC](https://help.galaxyproject.org/t/problems-regarding-file-upload-in-deseq2/15218 "2025-04-12T11:04:28Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![Sukanya\_Ghosh](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/sukanya_ghosh/32/7032_2.png) [@Sukanya\_Ghosh](https://help.galaxyproject.org/u/Sukanya_Ghosh)\ **Post date:** [April 12, 2025, 11:04am UTC](https://help.galaxyproject.org/t/problems-regarding-file-upload-in-deseq2/15218/1 "2025-04-12T11:04:28Z")
My count file collection is not appearing in the “Input” section whenever I am selecting the option “Select group tags corresponding to levels”. I would you to resolve the issue as soon as possible. ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/4/4ee396876711a6dce31ad3eb66a25b217b639878.png) Thank you ---
**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\ **Post date:** [April 13, 2025, 8:00am UTC](https://help.galaxyproject.org/t/problems-regarding-file-upload-in-deseq2/15218/2 "2025-04-13T08:00:53Z")
Hi @Sukanya_Ghosh, It seems you have individual count files in the history. Try DESeq2 with the default option, Select datasets per level. Check DESeq2 job setup in this tutorial: > **[Transcriptomics / Reference-based RNA-Seq data analysis / Hands-on:...](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html#identification-of-the-differentially-expressed-features)** > > Training material for all kinds of transcriptomics analysis. Hope that helps. Kind regards, Igor ---
**Author:** ![Sukanya\_Ghosh](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/sukanya_ghosh/32/7032_2.png) [@Sukanya\_Ghosh](https://help.galaxyproject.org/u/Sukanya_Ghosh)\ **Post date:** [April 13, 2025, 10:55am UTC](https://help.galaxyproject.org/t/problems-regarding-file-upload-in-deseq2/15218/3 "2025-04-13T10:55:50Z")
Whenever I am running the operation with the option “Select datasets per level”, I am receiving an error message as follows. ![image.png](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/7/72d476b8cbb9557a9362fc9f7ecf758576cd3bde.jpeg) Please help me resolve this issue. Thank you in advance ---
**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\ **Post date:** [April 14, 2025, 1:12am UTC](https://help.galaxyproject.org/t/problems-regarding-file-upload-in-deseq2/15218/4 "2025-04-14T01:12:35Z")
Hi @Sukanya_Ghosh Do you have replicates? DESeq2 requires replicates for reliable statistics. This error message appears when no replicates are present. For two conditions you need at least three samples, preferably more. Kind regards, Igor ---
**Author:** ![Sukanya\_Ghosh](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/sukanya_ghosh/32/7032_2.png) [@Sukanya\_Ghosh](https://help.galaxyproject.org/u/Sukanya_Ghosh)\ **Post date:** [April 14, 2025, 3:45am UTC](https://help.galaxyproject.org/t/problems-regarding-file-upload-in-deseq2/15218/5 "2025-04-14T03:45:21Z")
Okk I got it…thanks a lot ---
**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\ **Post date:** [April 14, 2025, 7:37am UTC](https://help.galaxyproject.org/t/problems-regarding-file-upload-in-deseq2/15218/6 "2025-04-14T07:37:03Z")
Hi @Sukanya_Ghosh, More info on the topic here explaining why replicates are required: > [@DESeq2 or EdgeR or Limma without replication](https://help.galaxyproject.org/t/deseq2-or-edger-or-limma-without-replication/2802/5): > > Thank you Nagul, but each factor I have only one sample, no replication, that why it have error. as I know edgeR can do without replication (use bioconductor) but in Galaxy can not do. If there are any solution, please tell me. Thank you so much Kind regards, Igor ---
**Author:** ![Sukanya\_Ghosh](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/sukanya_ghosh/32/7032_2.png) [@Sukanya\_Ghosh](https://help.galaxyproject.org/u/Sukanya_Ghosh)\ **Post date:** [April 15, 2025, 9:48am UTC](https://help.galaxyproject.org/t/problems-regarding-file-upload-in-deseq2/15218/7 "2025-04-15T09:48:29Z")
Thank you so much