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Hello! Please visit our most up to date repo at https://github.com/ncsa/NEAT. Currently the behavior for on-target regions is to use a 98/2 split for coverage, but it is not possible to get more fine-grained this (you can additionally set coverage to 0 in off target regions by using the discard off target flag). You can submit this as a feature request on the new repo, however.
Would it be possible to specify the relative expression levels of the targeted regions specified by -tr?
Thank you!
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