zpliu1126
zpliu1126
same problem here。。。
Thank you for your reply。 I'm not sure how many it have。 But I find this double intron retention events in a isoform，and it will result in stop coden earlyer。
I strongly recommend that you run the leafcutter in the container, which avoids unnecessary trouble in installing the leafcutter. I manually packaged a singularity container, maybe you can try it....
@andrewprzh "In the test document, HC04_A05031980 is the reference annotated gene that corresponds to the aforementioned AD1_HC04_A05_125890; while HC04_D05032280 corresponds to the aforementioned AD1_HC04_D05_496010. ### isoform annotated by IsoQuant [test_models.txt](https://github.com/user-attachments/files/15855891/test_models.txt)...
Dear @andrewprzh > If a novel isoform has a known intron chain, then TSS/TES positions are taken from the annotation, which is quite inaccurate. Perhaps one could choose TSS that...