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parklab / xTea

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
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Will the coverage of BAM files affect the xTea results? #110

Closed sidi-yang closed 3 months ago

sidi-yang commented 3 months ago

Hi Simon,

Just wondering will the coverage of BAM files affect the results?

Thank you!

simoncchu commented 3 months ago

It depends on the depth. In my earlier tests, the performance drops a lot when the depth is lower than 15x. But since most of the available samples having ~30x or higher depth, I didn't spend much time in optimization on low depth samples.

sidi-yang commented 3 months ago

Hi Simon,

Thank you for the answer. But what if one sample has a mean coverage of 30X while the other sample has a mean coverage 70X?

Do you think xTea will output more TEs when detecting samples with 70X coverage, compared with samples with 30X coverage?

Or will you say if the coverage is over than 30X, there is no need to dwell on the coverage?

Thank you very much!

simoncchu commented 3 months ago

It should be fine. The parameters are adjusted by depth automatically.