-i option seems to have no effect on filtering [intronIC v2.4.2]

[arabec]

Hi,

First of all, thank you for this very useful tool.

I seem to have encountered an issue with the -i option. I ran intronIC on human annotations (EnSEMBL release 110 GTF, GRCh38), both with and without this option enabled, but obtained identical results in both cases.

Below are the commands I used, along with the filtering section of the logs. From what I can see, introns located in alternative isoforms still appear to be filtered out even when using the -i option.

intronIC classify -g /mnt/data/arabec/refs/GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa -a /mnt/data/arabec/refs/GRCh38/Homo_sapiens.GRCh38.110.gtf -n Homo_sapiens -p 4

Total genes: 62,754, introns generated: 1,396,783
Intron Filtering Summary:
┌────────────────────────────┬────────────┬────────────┐
│ Category │ Included │ Excluded │
├────────────────────────────┼────────────┼────────────┤
│ Duplicates │ 0 │ 994,237 │
│ Too short │ 0 │ 99 │
│ Ambiguous bases │ 0 │ 0 │
│ Non-canonical │ 4,522 │ 0 │
│ Overlapping │ 0 │ 0 │
│ Alternative isoform │ 0 │ 171,225 │
├────────────────────────────┼────────────┼────────────┤
│ Total excluded │ │ 1,165,561 │
│ Retained for scoring │ │ 230,655 │
└────────────────────────────┴────────────┴────────────┘

intronIC classify -g /mnt/data/arabec/refs/GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa -a /mnt/data/arabec/refs/GRCh38/Homo_sapiens.GRCh38.110.gtf -n Homo_sapiens -i -p 4

Total genes: 62,754, introns generated: 1,396,783
Intron Filtering Summary:
┌────────────────────────────┬────────────┬────────────┐
│ Category │ Included │ Excluded │
├────────────────────────────┼────────────┼────────────┤
│ Duplicates │ 0 │ 994,237 │
│ Too short │ 0 │ 99 │
│ Ambiguous bases │ 0 │ 0 │
│ Non-canonical │ 4,522 │ 0 │
│ Overlapping │ 0 │ 0 │
│ Alternative isoform │ 0 │ 171,225 │
├────────────────────────────┼────────────┼────────────┤
│ Total excluded │ │ 1,165,561 │
│ Retained for scoring │ │ 230,655 │
└────────────────────────────┴────────────┴────────────┘

Could you please have a look at this behavior?

Thank you very much for your help.

Best regards,
Alexia

Conda environment details:
intronIC version: 2.4.2
Python version: 3.11.15

[glarue]

Hi @arabec thanks for raising this - definitely a bug from the v1 --> v2 move.

I've backported a fix to the new v2.4.3 release; please let me know if it's still giving you problems.

Also if you're planning on using it for extensive work in the near future, I'm currently finalizing a new release that will incorporate some additional multi-species training data and a few other improvements that might be worth waiting for depending on your use-case.

[arabec]

Hi,

Thank you for your quick response. The solution works perfectly.
I’ll wait a bit as suggested. Thanks again for the information.

Best regards,
Alexia

[glarue]

@arabec I've just pushed the new v3 release, in case you're still thinking about using it directly. Also, depending on what species you're planning to look at, there may already be data in the new version of the WtMTA db, which uses intronIC v3.0.0 for it's underlying data.

[arabec]

Hi,

Sorry for the late reply. Thanks for the update and for this very useful database!

Best regards,
Alexia