How to set alignIntronMax parameter in RNA STARSolo in Galaxy?

usegalaxy.org support
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1

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?

2

Hi @paige_kulzer
I am wondering whether data is from scRNA-seq or snRNA-seq?
Best,
Pavan

3

Hi Pavan,

I’m working with scRNA-Seq data!

4

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.

5

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?

6

They’re available on the EU server. Sorry, I should have asked you first. Which server are you using?

7

Ah, I’m on the main usegalaxy.org server! Is it possible to update STARSolo on this server, too?

8

@jennaj I created a PR here to update the tool to the latest version. Can you please take care of the installation on .org?

9

Thank you so much, Pavan! I’ve now been able to run the new version of RNA STARSolo on both Galaxy servers.