Features on the (-) strand marked "Downstream" but are actually upstream

loosolab / UROPA

Universal RObust Peak Annotator

https://uropa-manual.readthedocs.io/

MIT License

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Features on the (-) strand marked "Downstream" but are actually upstream #3

Closed mcsimenc closed 3 years ago

mcsimenc commented 3 years ago

Thanks for developing UROPA!

When I look at genes where the associated peak is marked "Downstream" in my UROPA output in a genome browser, I see that the peaks are upstream of the genes, which are on the - strand. Could this be a bug where strand is not taken into account? In the docs it says upstream/downstream is relative to strand, but my output does not reflect that.

Best,

Matt

msbentsen commented 3 years ago

Hi Matt, You are completely right - this was a bug. There was an error in how the assignment of downstream/upstream was set in comparison to the feature anchor. We just released a fix in uropa 3.5.3, where the strand is taken into account. Sorry for the inconvenience! Best Mette

mcsimenc commented 3 years ago

Hi Mette, thank you for the speedy response! I'll upgrade my UROPA installation.