Transfer single cell RNAseq data analyzed in Seurat into GSEA

Hello,

I was wondering if there is a way to transfer single cell RNAseq data analyzed in Seurat into GSEA. I know that one of the supported file formats is txt (tab delim text), so I saved the list of gene obtained in Seurat with the argument FindAllMarkers as txt, but when I try to load it on GSEA I get the following error:

---- Full Error Message ----
There were errors: ERROR(S) #:1
Parsing trouble
java.lang.IndexOutOfBoundsExcept …

---- Stack Trace ----

of exceptions: 1

------Index: 0, Size: 0------
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.rangeCheck(ArrayList.java:657)
at java.util.ArrayList.get(ArrayList.java:433)
at edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:102)
at edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:87)
at edu.mit.broad.genome.parsers.ParserFactory.readDatasetTXT(ParserFactory.java:202)
at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:749)
at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:726)
at edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:52)
at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at javax.swing.SwingWorker.run(SwingWorker.java:334)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

I am clearly doing something wrong, but I can’t figure it out and I am very new at the topic.
I hope you can help me with this. Thank you for your time.
Michela

Hi @frascolim,

Your GitHub Community Forum post was moved to a different board that fits your topic of discussion a bit better. This means you’ll get better engagement on your post, and it keeps our Community organized so users can more easily find information.

You can now find your Topic in the Project Development Help and Advice board.

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Let me know if you have any other questions or if I can help with anything else.

Cheers!