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rmhubley / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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The sum of the subclasses does not correspond to the sum of the DNA transposons. #228

Closed aijigekoukou-shen closed 7 months ago

aijigekoukou-shen commented 11 months ago

Hi rmhubley,

I hope this email finds you well. I am currently facing a small issue while annotating repetitive sequences in my genome using RepeatMasker. The tbl file shows that my genome contains 23.70% DNA transposons, but the sum of various subtypes does not match the total. I have merged the results from EDTA and RepeatModeler to annotate the repetitive sequences and have modified the names to match the format recognized by RepeatMasker.

I would greatly appreciate your assistance in resolving this matter.

Thank you.

Shen

Below is my tbl file:

*================================================== number of length percentage elements occupied of sequence

Retroelements 138177 104587050 bp 23.10 % SINEs: 2 72 bp 0.00 % Penelope 0 0 bp 0.00 % LINEs: 6088 4014252 bp 0.89 % CRE/SLACS 0 0 bp 0.00 % L2/CR1/Rex 0 0 bp 0.00 % R1/LOA/Jockey 0 0 bp 0.00 % R2/R4/NeSL 0 0 bp 0.00 % RTE/Bov-B 51 4145 bp 0.00 % L1/CIN4 6037 4010107 bp 0.89 % LTR elements: 132087 100572726 bp 22.21 % BEL/Pao 0 0 bp 0.00 % Ty1/Copia 34660 23685496 bp 5.23 % Gypsy/DIRS1 91140 73234295 bp 16.18 % Retroviral 0 0 bp 0.00 %

DNA transposons 403918 107314424 bp 23.70 % hobo-Activator 155253 32413680 bp 7.16 % Tc1-IS630-Pogo 25342 6913640 bp 1.53 % En-Spm 0 0 bp 0.00 % MuDR-IS905 0 0 bp 0.00 % PiggyBac 0 0 bp 0.00 % Tourist/Harbinger 7809 1770147 bp 0.39 % Other (Mirage, 0 0 bp 0.00 % P-element, Transib)

Rolling-circles 1192 938990 bp 0.21 %

Unclassified: 114748 29476293 bp 6.51 %

Total interspersed repeats: 241377767 bp 53.32 %

Small RNA: 0 0 bp 0.00 %

Satellites: 23 6084 bp 0.00 % Simple repeats: 113 5162 bp 0.00 % Low complexity: 0 0 bp 0.00 % ==================================================**

JMStorer commented 10 months ago

Greetings!

DNA transposons 403918 107314424 bp 23.70 % hobo-Activator 155253 32413680 bp 7.16 % Tc1-IS630-Pogo 25342 6913640 bp 1.53 % En-Spm 0 0 bp 0.00 % MuDR-IS905 0 0 bp 0.00 % PiggyBac 0 0 bp 0.00 % Tourist/Harbinger 7809 1770147 bp 0.39 % Other (Mirage, 0 0 bp 0.00 % P-element, Transib)

The bolded line is NOT the sum total of the subtypes, but rather a category by itself. This describes the elements identified as some type of DNA element, but the subtype/subfamily could not be determined.

I hope this helps!