nuno-agostinho
commented
3 years ago Hi Nick! I am very sorry for this inconsistency and thank you for pointing it out.
The event ID in the top right (e.g. A5SS_1_-_1274742_1274667_1274033_DVL1) has the event coordinates: one for each exon needed to calculate PSI. The coordinate of the exon used as reference for PSI quantification is always in the middle (in the given example, the exon that ends in position 1274667). That should always be the orange exon in both plots:
After some quick testing, the transcript plot colours in orange the right exon, whereas the schematic is colouring the wrong exon in AFE and A5SS events.
I will update psichomics with this corrected after doing some more tests. In the meantime, please disregard the schematic for these event types.
If you have any further questions, please ask me away.
Once again, I am sorry for the inconvenience. Thank you!
nick-webster
Hi, I have a question about interpreting individual AS results.
For SE it seems straight forward. The SE exon is colored orange in the PSI plot and in the transcript plot, so no problem. The A3SS plot has the orange exon downstream in both PSI and transcript plots, so again no problem.
But with AFE, the schematic of the AFE event shows the downstream first exon in orange so I interpret the PSI plot to indicate that the icon with the orange exon included indicates use of the downstream first exon, i.e. downstream exon is the alternative. But if I look at the transcript information, the upstream first exon is shaded orange and the downstream one blue, i.e. the upstream exon is the alternative exon. Which is correct? I think this also causes problems with the A5SS interpretation. The upstream SS is labeled orange in the schematic, but it is the downstream SS labeled orange in the transcript plot. This is confusing as it completely reverses the conclusions.
Thanks, Nick