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allow user to set splicing window differently based on acceptor/donor end #135

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yang-yangfeng opened this issue Jan 23, 2020 · 1 comment

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@yang-yangfeng
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per reviewer comment

@kcotto
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kcotto commented Oct 2, 2020

Comment from reviewer:
"However, RegTools is not as flexible as existing genomic range software. For example, RegTools “variant annotate” treats the donor and acceptor ends of an intron or exon in the same way. But, users may have strong biological priors to treat the donor and acceptor ends of an intron differently (the acceptor end of an intron contains the branchpoint and the polypyrimidine tract splice signals). In contrast, it is simple to extend genomic range differently downstream and upstream with respect to strand."

Ideally, the results would look something like -e_donor 5 and -e_acceptor 13.

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