Suggestions for Reliable Alternative Splicing Workflow in Galaxy?

usegalaxy.org support
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Hi, I have RNA-seq datasets from control and treated samples, and I’m planning to perform an alternative splicing analysis, particularly interested in the differential expression pattern of individual exons of my GOIs. I followed the “Genome-wide alternative splicing analysis” workflow, but I got stuck at the STAR alignment step due to excessive RAM requirements. As a workaround, I tried using HISAT2 instead, but StringTie froze and did not proceed. Could anyone suggest a reliable workflow or alternative approach for performing alternative splicing analysis in Galaxy?

Thank you!

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Welcome @vulcanica

Would you like to troubleshoot this part?

If a tool is running out of memory resources during job execution that usually indicates a data problem. → FAQ: Understanding 'exceeds memory allocation' error messages

For these tools, reference data is usually the problem. Either mixed up assemblies (discussion → Reference genomes at public Galaxy servers: GRCh38/hg38 example) or a formatting problem (help → FAQ: Extended Help for Differential Expression Analysis Tools).

Then, for one of the downstream tools we are still working on increasing the memory allocation at UseGalaxy.org but you can work at UseGalaxy.eu instead if needed. You don’t need to start over, just move your samples over. → IsoformSwitchAnalyzeR Import Data: Memory Allocation - #6 by AAA-3

Some of this depends on the genome you are working with. Is this for human? If yes, the resources needed can be considerable, and the public server you are working at may be important. Would you like to share your history back? We’ll be able to rule out technical issues and make more specific suggestions about how to proceed. → How to get faster help with your question

Let’s start there! :slight_smile: