pigeon isoform number uncorrect

[suyanan]

Hi,

I use command pigeon report test_classification.filtered_lite_classification.txt test.saturation.txt, getting test.saturation.txt bellow:

Then, I figure out that the genes number is same with 7th column in test_classification.filtered_lite_classification.txt, but the isoform is not with 1th column.
And the isoform is same with the total_unique_transcripts in test_classification.filtered.report.json. just FSM+ISM > total_unique_transcripts, Your support team also mentioned that the total_uniq_transctipts is not correct in smrtlink v13.1 I used here.

Is the isoform stat method special, or uncorret ?
Best wishes.

[jacp1]

I see this as well. The max number of unique genes (known and novel) reported in the isoseq_saturation.txt file matches the pigeon_filtered_classification file. But the max number of unique transcripts is much lower than the total number of rows in the pigeon_filtered_classification file. This is using the GUI workflow for SmrtLink 25.1 default settings, pooled samples