hello, I'm analyzing my genome to find transposon. I make the first analysis with repeatmasker and here there are some elements that I found and their abundance. My question is: what does it mean the ? next to some elements? It is an error of repeatmasker or are elements recognized by repeatmasker that could be considered as....?
THis is the table:
table:
DNA? DNA/hAT-Ac DNA/hAT-Charlie DNA/hAT-Tag1 DNA/hAT-Tip100
5 84 276 2 71
DNA/PiggyBac DNA/TcMar-Mariner DNA/TcMar-Tc1 LINE/CR1 LINE/Dong-R4
10 601 17 16 196
LTR/ERV1 LTR/ERVK LTR/ERVL LTR/Gypsy LTR/Gypsy?
2 16 2 49 128
snRNA srpRNA tRNA Unknown
39 7 102 1
1 answer
The response from Robert Hubley (one of the developers of this tool) at SEQanswers in 2013:
The "?" following either a class for subclass is an indication that the curator is not confident in the call of the class or subclass. As we learn more about the element in question the classification is either changed or the "?" designation is removed.
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Not directly related to your question but would it be possible to check the formatting of that table? Or is this an R-object or such (hence the 'R' tag on your question)
Yes it is an R object but I cannot explain the LTR/gypsy with and without ?
no expert but my guess would be 'known' and 'putative/potential' elements .
This also does not look like any of the ReepatMakser output files. How did you get this in that R-object? aka, what steps have you done between running RepeatMaker and printing this R object?