Hello splicing specialists,
We have performed long-read sequencing and SUPPA2 analysis for splicing events between knock-down vs. control cells, and are looking for the best ways to visually assess the quality of our statistical tests at the individual gene level. Is there a good tool for splice junction plots or switch plots to display both transcript coverage data, together with event information (percent spliced in or delta percent spliced in) from long-read seq data? Looking around, I see mostly short-read seq data presentation that might use tools not matched to our case.
For example, panel E from this figure: https://www.science.org/cms/10.1126/scitranslmed.ade2774/asset/32891b90-b4e6-4704-9f78-ad1827e20e9e/assets/images/large/scitranslmed.ade2774-f2.jpg Coming from DOI: https://doi.org/10.1126/scitranslmed.ade2774
Shows the information we are looking to visualize. I don't see the tool for this plot in the paper.
Many thanks!
Alison
IGV can view coverage and splice junction sashimi plots. However the plot in the paper looks like it was made with miso. https://miso.readthedocs.io/en/fastmiso/sashimi.html