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?
Hi @paige_kulzer
I am wondering whether data is from scRNA-seq or snRNA-seq?
Best,
Pavan
Hi Pavan,
I’m working with scRNA-Seq data!
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.
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?
They’re available on the EU server. Sorry, I should have asked you first. Which server are you using?
Ah, I’m on the main usegalaxy.org server! Is it possible to update STARSolo on this server, too?
@jennaj I created a PR here to update the tool to the latest version. Can you please take care of the installation on .org?
Thank you so much, Pavan! I’ve now been able to run the new version of RNA STARSolo on both Galaxy servers.