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XiaoTaoWang / EagleC

A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
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Non human genomes #23

Closed luciaalvarez95 closed 1 year ago

luciaalvarez95 commented 1 year ago

Hi!

Amazing tool! However, I was wondering....Can it be used with non-human samples? Like other mammalian species?

Thanks

XiaoTaoWang commented 1 year ago

Yes, EagleC can be used to detect SVs in non-human samples by specifying "--genome other" when running the predictSV or predictSV-single-resolution commands. However, it is important to note that the predictions in non-human samples may contain spurious calls, particularly those associated with centromeres and telomeres. To improve the accuracy of your predictions, you may need to manually examine calls with breakpoints located near genome assembly gaps (e.g., <250kb).

luciaalvarez95 commented 1 year ago

Many thanks for the reply :))) I have tried it but it doesn't seem to work properly since no SVs have been detected (and no errors) . Do the chromosomes need to be labelled has chr1, chr2.....,X?

XiaoTaoWang commented 1 year ago

No, the prefix "chr" is not required for EagleC to be run. Did you get any output? Can you show me the content in the log file?

luciaalvarez95 commented 1 year ago

Hi! I have found out the problem, chr names have to be specified in -C flag (and I didn't do it) Now it has been running for a while! Many thanks for help :)