diffmod.table missing majority of positions

[JannesSP]

Dear xpore developers,

I ran xpore on two SARS-CoV-2 samples to compare variant differences.
After running xpore dataprep and then xpore diffmod I only receive information for about 2500 out of 30000 genomic positions.
I followed your guide to prepare the bam and nanopolish files.
Then I used only default parameters for the dataprep like this:
xpore dataprep --eventalign ventalign_result.csv --out_dir /dataprep --n_processes 12
Do you have any idea what might went wrong?
Or it this a expected behavior for the uneven and special coverage that Coronaviruses have?

Kind Regards,
Jannes Spangenberg

[yuukiiwa]

Hi @JannesSP,

The reason why you are getting 2,500 out of 30,000 genomic positions is that xpore filters out the sites that do not have a significant difference between the two conditions.

Another thing that could have happened is that you included the following in the config.yml file to xpore diffmod:

method:
    prefiltering:
        method: t-test
        threshold: <P_VALUE_THRESHOLD>

This does prefiltering, which significantly lowers the number of sites included in xpore diffmod output.

Thanks!

Best wishes,
Yuk Kei

[JannesSP]

Hi @yuukiiwa,

I did not include a prefiltering in the config.yml.
So it seems that xpore filters a lot of positions.
Is it possible to disable this filtering?

Kind Regargs,
Jannes Spangenberg

[yuukiiwa]

Hi @JannesSP,

Sorry for the delayed reply!

I will talk to @ploy-np to potentially push a release with a flag to skip the filtering.

Thanks!

Best wishes,
Yuk Kei

[JeremyQuo]

Hello, I met the same problem and I modified the code to check the number of the position that will be used to compare in diffmod.py . I found that most sites will not join the comparison, which is not related to the filter. Can you tell me that how to solve this problem

[yuukiiwa]

Hi @JeremyQuo,

xpore diffmod does internal filtering of sites if the distributions of the two conditions are overlapping too much from each other. @ploy-np and I are still considering whether to skip the filtering as it would produce too much noise in the diffmod.table.

Thanks!

Best wishes,
Yuk Kei