Using STARsolo Output

[I-am-Shir]

Hello,
I see that the samplesheet is expecting a CellRanger Output Directory Path.
Is there a way to use data generated with STAR, specifically STARsolo, instead?

Sincerely,
Shir

[mschilli87]

שלום @I-am-Shir,

Please have a look at #19 for some discussion regarding what SCALPEL needs and how custom formats might be provided in a future version.
I have not worked with STARsolo, so I don't know how it formats its output.
If you could provide us with an overview how the relevant information is provided in its output (comparing to CellRanger and/or Drop-seq tools), it will be easier for us to determine if it is already possible to feed it into SCALPEL (and help you do so) or if (and what) changes we'd have to implement to make it work.

[mschilli87]

@I-am-Shir: Are you still interested in this?

[I-am-Shir]

@mschilli87 Hey, I fitted the tool to work for my STARsolo data, I'm hoping to go over it to make sure it will work for both CellRanger data and STARsolo and then hopefully you'll be able to integrate it so it will work for more people.

Sincerely,
Shir

[mschilli87]

@I-am-Shir: Great to hear. I'll leave this open then. Feel free to ask for help here and/or share whatever you have. A PR would be most welcome but we could also work on the integration ourselves or together based on your input. Whatever works best for you.