# How to set alignIntronMax parameter in RNA STARSolo in Galaxy? **URL:** \ **Category:** usegalaxy.org support\ **Tags:** tool-help, single-cell, rna\_starsolo\ **Created:** [May 29, 2025, 3:29pm UTC](https://help.galaxyproject.org/t/how-to-set-alignintronmax-parameter-in-rna-starsolo-in-galaxy/15580 "2025-05-29T15:29:42Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![paige\_kulzer](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/paige_kulzer/32/5424_2.png) [@paige\_kulzer](https://help.galaxyproject.org/u/paige_kulzer)\ **Post date:** [May 29, 2025, 3:29pm UTC](https://help.galaxyproject.org/t/how-to-set-alignintronmax-parameter-in-rna-starsolo-in-galaxy/15580/1 "2025-05-29T15:29:43Z")
Hello! I’m attempting to align my scRNA-Seq data using RNA STARsolo in Galaxy. I’m seeing a lot of alignments that span multiple genes with spurious introns. I believe that reducing the maximum intron length parameter would help improve the alignment quality. In standard RNA STAR, I know I can use the --alignIntronMax parameter to do this, but I’m having a hard time finding a similar parameter for RNA STARSolo. Is there an equivalent available in the RNA STARsolo tool on Galaxy? ---
**Author:** ![pavanvidem](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/pavanvidem/32/1687_2.png) [@pavanvidem](https://help.galaxyproject.org/u/pavanvidem)\ **Post date:** [May 29, 2025, 6:15pm UTC](https://help.galaxyproject.org/t/how-to-set-alignintronmax-parameter-in-rna-starsolo-in-galaxy/15580/2 "2025-05-29T18:15:35Z")
Hi @paige_kulzer I am wondering whether data is from scRNA-seq or snRNA-seq? Best, Pavan ---
**Author:** ![paige\_kulzer](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/paige_kulzer/32/5424_2.png) [@paige\_kulzer](https://help.galaxyproject.org/u/paige_kulzer)\ **Post date:** [May 29, 2025, 7:05pm UTC](https://help.galaxyproject.org/t/how-to-set-alignintronmax-parameter-in-rna-starsolo-in-galaxy/15580/3 "2025-05-29T19:05:48Z")
Hi Pavan, I’m working with scRNA-Seq data! ---
**Author:** ![pavanvidem](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/pavanvidem/32/1687_2.png) [@pavanvidem](https://help.galaxyproject.org/u/pavanvidem)\ **Post date:** [June 1, 2025, 9:53am UTC](https://help.galaxyproject.org/t/how-to-set-alignintronmax-parameter-in-rna-starsolo-in-galaxy/15580/4 "2025-06-01T09:53:54Z")
We added all the algorithmic parameters of STAR into STARSolo. The new version should be online by tomorrow. There should be a new section called “Algorithmic settings” where you can fine-tune more settings. ---
**Author:** ![paige\_kulzer](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/paige_kulzer/32/5424_2.png) [@paige\_kulzer](https://help.galaxyproject.org/u/paige_kulzer)\ **Post date:** [June 4, 2025, 12:37pm UTC](https://help.galaxyproject.org/t/how-to-set-alignintronmax-parameter-in-rna-starsolo-in-galaxy/15580/5 "2025-06-04T12:37:16Z")
Thank you so much! I see an Algorithmic Parameters section for the RNA STAR tool but I’m not seeing this same section for RNA STARSolo as of a few days later. Is the new version still being put online or am I missing it? ---
**Author:** ![pavanvidem](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/pavanvidem/32/1687_2.png) [@pavanvidem](https://help.galaxyproject.org/u/pavanvidem)\ **Post date:** [June 4, 2025, 12:54pm UTC](https://help.galaxyproject.org/t/how-to-set-alignintronmax-parameter-in-rna-starsolo-in-galaxy/15580/6 "2025-06-04T12:54:22Z")
They’re available on the EU server. Sorry, I should have asked you first. Which server are you using? ---
**Author:** ![paige\_kulzer](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/paige_kulzer/32/5424_2.png) [@paige\_kulzer](https://help.galaxyproject.org/u/paige_kulzer)\ **Post date:** [June 4, 2025, 12:56pm UTC](https://help.galaxyproject.org/t/how-to-set-alignintronmax-parameter-in-rna-starsolo-in-galaxy/15580/7 "2025-06-04T12:56:51Z")
Ah, I’m on the main [usegalaxy.org](http://usegalaxy.org) server! Is it possible to update STARSolo on this server, too? ---
**Author:** ![pavanvidem](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/pavanvidem/32/1687_2.png) [@pavanvidem](https://help.galaxyproject.org/u/pavanvidem)\ **Post date:** [June 4, 2025, 1:57pm UTC](https://help.galaxyproject.org/t/how-to-set-alignintronmax-parameter-in-rna-starsolo-in-galaxy/15580/8 "2025-06-04T13:57:44Z")
@jennaj I created a PR [here](https://github.com/galaxyproject/usegalaxy-tools/pull/1006) to update the tool to the latest version. Can you please take care of the installation on .org? ---
**Author:** ![paige\_kulzer](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/paige_kulzer/32/5424_2.png) [@paige\_kulzer](https://help.galaxyproject.org/u/paige_kulzer)\ **Post date:** [June 10, 2025, 7:48pm UTC](https://help.galaxyproject.org/t/how-to-set-alignintronmax-parameter-in-rna-starsolo-in-galaxy/15580/9 "2025-06-10T19:48:50Z")
Thank you so much, Pavan! I’ve now been able to run the new version of RNA STARSolo on both Galaxy servers.