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bug report: junction extract tool should not count overlapping reads as double support for a junction #187
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- added 5 commits that reference this issue
on Jul 1, 2024 - added a commit that references this issue
on Sep 19, 2024
In the current implementation, read-mates can provide 2 "counts" to the same junction if they both span it. This results in inflated counts and therefore inflated significance when downstream tools consider the counts.
I would like to advocate for each queryname to be able to provide a maximum of 1 count towards any single junction. This must be implemented carefully so memory use doesn't spike too much.