akahles
commented
3 years ago Thank you for looking into SplAdder. When the splicing graphs grow very complex, the detection of alternative events can be computationally expensive, as the number of possible paths in the graph grows exponentially. This is usually driven by very few overly complex genes (which can be caused by the SplAdder heuristic itself, but also by artifacts in the input data). One can cap the handling of these outliers with the --no-extract-ase parameter. The default is at 500. I would recommend lowering this threshold further (e.g.,300) for events like mult_exon_skip.
Hello guys, An issue encounter to me, I don't know how to fix it. When I use spladder build mode to detect alternative splicing events, the first 3 steps, Single graphs , Merged graph, and Quantification work fine. However, when I continue the 4th step with extracting all 6 events (--extract-ase), it becomes really slow, and even I run the work for a day I still can't get results. I have tested other sample data, it will take about 5~10 minutes to get all events at 4th step if all data is ready. So I try to extract event one by one, I find only the mult_exon_skip event can't be extracted and all other events can be got quickly. I was wondering, is it because the mult_exon_skip event can't be found in the data? or complexity? The work keeps running and shows no error. Dose anyone have the same issue? I will really appreciate it if someone can give me a hint.