Open zpliu1126 opened 1 month ago
@zpliu1126
Indeed, an interesting case, but it's really hard to tell only using screenshots. Could you maybe send me these transcripts, associated reads and their assignments from read_assignments.tsv?
Best Andrey
@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.
Thanks, will take a look!
Hi~ Andrey, I am using IsoQuant's v3.3.1 Reference-base model for Isoform annotation in polyploid species and updating my gff3 annotation file. To check the accuracy of the annotation, I visualized the alignment results of short and long reads in IGV. However, it seems that IsoQuant did not annotate the isoforms containing RI in AD1_HC04_A05_125890. But for the orthologous gene AD1_HC04_D05_496010 of AD1_HC04_A05_125890, IsoQuant was able to detect isoforms containing RI. I also checked the annotation gff3 file before updating, and both genes only had isoforms annotated without RI; but IsoQuant only updated the corresponding annotations in AD1_HC04_D05_496010. I want to know what might be the reason for this situation?
IGV show for AD1_HC04_A05_125890
IGV show for AD1_HC04_D05_496010
Best zpliu