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hollygene / TE_MA

S. paradoxus TE MA experiment
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Plot each chromosome with the TE locations and coverage for each sample #7

Open hollygene opened 4 years ago

hollygene commented 4 years ago

Using karyoploteR to plot each chromosome with TE locations and coverage for each sample

Want: Graph of each chromosome, with locations of TEs marked and coverage graphs above

hollygene commented 4 years ago

https://github.com/hollygene/TE_MA/blob/a25698efe893cab33af8887bd68aa3535fd20589/R/TE_MA.Rmd#L345

cbergman commented 4 years ago
hollygene commented 4 years ago

I plotted chromosmes and lines that we determined to be segmental aneuploidies from other depth graphs, with their TE locations, using karyoploteR

Screen Shot 2020-05-19 at 10 46 59 AM Screen Shot 2020-05-19 at 10 47 36 AM Screen Shot 2020-05-19 at 10 48 06 AM Screen Shot 2020-05-19 at 10 48 49 AM Screen Shot 2020-05-19 at 10 49 33 AM Screen Shot 2020-05-19 at 10 55 26 AM

Most of the segmental duplications/deletions have TEs right at the breakpoint! :)

hollygene commented 4 years ago

Code to get those graphs is in a function in R here: https://github.com/hollygene/TE_MA/blob/27a573006325e4a8d129c5ea1a01e85bbe6b2516/R/TE_MA.Rmd#L483