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For APA usage lengthen or shorten ? #9

Open Frank-Passerby opened 2 years ago

Frank-Passerby commented 2 years ago

Dear sir, After reading the full text and running the code, we did not find objective indicators to objectively evaluate APA lengthening or shortening? May we know how did you evaluate APA usage lengthen or shorten in SCAPTURE? Many thanks!

liguowei-CAS commented 2 years ago

Hi, To evaluate APA lengthening or shortening, please follow the Vignette. We offer two metrics to calculate APA usage, one is RED (Relative Expression Difference score, log2(distal PAS/proximal PAS)), and the other is PUI (like PPUI or PDUI: Percentage of Proximal/Distal Poly(A) Usage Index).

rpghjs commented 2 years ago

Dear sir， I am appreciate that you offer two metrics to calculate APA usage. When I use red to evaluate APA usage length or shorten , I have some question. Dose the high red mean shorten? the low red mean lengthen? Dose the red score have threshold to evaluate APA usage lengthen or shorten? Actually I found that my datasets just have a part of feature (gene) to calculate the red score.When I want to explore the APA usage in gene levels ,could I subset the genes in useful calculate? Many thanks!