An inaccurate annotation

[zpliu1126]

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

[andrewprzh]

@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

[zpliu1126]

@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

read assignments

test_read_assignments.txt

[andrewprzh]

Thanks, will take a look!