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diffmod.table missing majority of positions
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
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
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
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
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
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