# Why can’t separate files be used in FASTP? Creating a paired end collection folder (data shapes and organization) **URL:** \ **Category:** usegalaxy.org support\ **Tags:** collections, fastp, collection-shape\ **Created:** [October 1, 2025, 11:57am UTC](https://help.galaxyproject.org/t/why-can-t-separate-files-be-used-in-fastp-creating-a-paired-end-collection-folder-data-shapes-and-organization/16329 "2025-10-01T11:57:27Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![H1889](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/h1889/32/6022_2.png) [@H1889](https://help.galaxyproject.org/u/H1889)\ **Post date:** [October 1, 2025, 11:57am UTC](https://help.galaxyproject.org/t/why-can-t-separate-files-be-used-in-fastp-creating-a-paired-end-collection-folder-data-shapes-and-organization/16329/1 "2025-10-01T11:57:27Z")
Hi. I have used FASTP in Galaxy many times and before I could select single, paired, or paired-end collection, so why can I now only use single or paired-collection? Why can’t both files (forward and reverse) be used independently? With the paired option I could select forward file and then reverse file without making a paired-collection. I think this also happens in other programs. Is it a problem with the tool itself or with Galaxy? Thanks Greetings ---
**Author:** ![H1889](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/h1889/32/6022_2.png) [@H1889](https://help.galaxyproject.org/u/H1889)\ **Post date:** [October 1, 2025, 12:14pm UTC](https://help.galaxyproject.org/t/why-can-t-separate-files-be-used-in-fastp-creating-a-paired-end-collection-folder-data-shapes-and-organization/16329/2 "2025-10-01T12:14:50Z")
![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/9/99cb78b6afb7454b60e8be5240d6eeac77b64f7f.png) ---
**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 1, 2025, 4:55pm UTC](https://help.galaxyproject.org/t/why-can-t-separate-files-be-used-in-fastp-creating-a-paired-end-collection-folder-data-shapes-and-organization/16329/3 "2025-10-01T16:55:10Z")
Hi @H1889 The change to using a collection for paired inputs was intentional. → [Missing "paired" input for fastp tool - #5 by bernt-matthias](https://help.galaxyproject.org/t/missing-paired-input-for-fastp-tool/14750/5) If you are not sure how to organize your data into a paired-end collection, I posted a little movie last week to demonstrate how to do this (works for any tool that accepts this data shape). > [@Collection folder VIDEO: How to create a single or paired end dataset collection folder (shapes and organization)](https://help.galaxyproject.org/t/collection-folder-video-how-to-create-a-single-or-paired-end-dataset-collection-folder-shapes-and-organization/16296/2): > > I’m guessing that you might still need to organize the reads into a paired end collection folder. > > Here is a little movie showing how to do it. Let us know if it helps! 🙂 * * * The “why” has to do with how sensitive this tool’s parameters/actions are dependent on paired end read data being input _per sample_ and processed together. A collection folder achieves that and make it much easier to include in a workflow. I didn’t hide the original datasets but you can to simplify the history. Or, not! This is your choice and you can always unhide collection dataset later on if you want these as individual datasets again. Please see the full post for more details + tutorials and let us know if you have any questions! 🙂 For the older versions that supported individual datasets for paired end data, these are still hosted! Go back about 8 versions to **0.24.0+galaxy3** → [FAQ: Changing the tool version](https://training.galaxyproject.org/training-material/faqs/galaxy/tools_change_version.html). Just keep in mind that tool releases are static for reproducibility reasons. So, if any new functionality has since been added or bug fixes applied, those won’t be back ported to the older releases. The change log can be reviewed at: Tool form → Options → See in Toolshed → Development repository link (usually a link out to Github) → tool.xml file → then History. For **fastp** , this would be here: [History for tools/fastp/fastp.xml - galaxyproject/tools-iuc · GitHub](https://github.com/galaxyproject/tools-iuc/commits/main/tools/fastp/fastp.xml) ---
**Author:** ![H1889](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/h1889/32/6022_2.png) [@H1889](https://help.galaxyproject.org/u/H1889)\ **Post date:** [October 1, 2025, 7:45pm UTC](https://help.galaxyproject.org/t/why-can-t-separate-files-be-used-in-fastp-creating-a-paired-end-collection-folder-data-shapes-and-organization/16329/4 "2025-10-01T19:45:50Z")
Thanks for the explanation, but I do not understand why eliminate that option, is it necessary? Tipically after a cleaning of the reads with FASTP, one run , for example, UNICYCLER that needs the R1 and R2 files not combined into one dataset. is it possible to separate the files after FASTP? sorry for the inconvenince. ---
**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 1, 2025, 9:51pm UTC](https://help.galaxyproject.org/t/why-can-t-separate-files-be-used-in-fastp-creating-a-paired-end-collection-folder-data-shapes-and-organization/16329/5 "2025-10-01T21:51:12Z")
For the question, you are not alone! Anyone is welcome to comment on the Github ticket in this topic or to start a new one. > [@jennaj](#): > > The change to using a collection for paired inputs was intentional. → [Missing “paired” input for fastp tool - #5 by bernt-matthias](https://help.galaxyproject.org/t/missing-paired-input-for-fastp-tool/14750/5) But the bigger idea is to use collections, and yes, you can modify collection shapes any way that you want to. If you currently have paired end, then **Unzip collection** or **Flatten collection** are common transformations. Both produce a list but are slightly different. Each have a graphic in the tool form Help explaining what they do so you can see the difference. ---
**Author:** ![H1889](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/h1889/32/6022_2.png) [@H1889](https://help.galaxyproject.org/u/H1889)\ **Post date:** [October 1, 2025, 10:50pm UTC](https://help.galaxyproject.org/t/why-can-t-separate-files-be-used-in-fastp-creating-a-paired-end-collection-folder-data-shapes-and-organization/16329/6 "2025-10-01T22:50:57Z")
I understand your point of vew, however, there is no harm in leaving the option of having the two files separately. As I mentioned before, there are many tools that need the two files separately, so allowing the two files separately does not harm the system or users. I suggest leaving the three options: single, two files, and paired collection. Best regards