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Confusion about transposable element filename #481

Closed yaaminiv closed 5 years ago

yaaminiv commented 5 years ago

@kubu4 The transposable element file you generated using only C. virginica as your species has "Cg" at the end of the filename:

screen shot 2018-11-13 at 3 00 56 pm

I know you also used C. gigas to identify transposable elements. I may just be paranoid, but is the file linked here from when you used C. virginica or C. gigas to identify transposable elements? In this issue, you said the linked file was from when you used C. virginica. I just wanted to double check since Cg could mean C. gigas!

kubu4 commented 5 years ago

Cg means C.gigas (@sr320 labelled these, so I can't be 100% certain, but I'm 99.9% certain). Sorry for the typo in the previous issue. I've gone back and edited that comment for clarity.

yaaminiv commented 5 years ago

@kubu4 Thank you!

That brings me to a related question for @sr320: how can I access the TE generated from the C. virginica genome? Or is that a file that I would not want to use file for BEDtools analysis of DML and DMR?

sr320 commented 5 years ago

It’s is @ http://onsnetwork.org/kubu4/2018/08/28/transposable-element-mapping-crassostrea-virginica-genome-cvirginica_v300-using-repeatmasker-4-07/

But prefer ALL and Cg - as you see Cv annotation is sparse