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I have been trying to detect, classify the transposable element in my eukaryotic non-referenced genome, (denovo)
I'm using RepeatMasker to do the job but whenever I run the tools the results shows only simple repeat and satellites.
where I'm trying to detect LTR elements, LINEs, SINES
bases masked: 33282890 bp ( 1.66 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
SINEs: 0 0 bp 0.00 %
Alu/B1 0 0 bp 0.00 %
MIRs 0 0 bp 0.00 %
LINEs: 0 0 bp 0.00 %
LINE1 0 0 bp 0.00 %
LINE2 0 0 bp 0.00 %
L3/CR1 0 0 bp 0.00 %
RTE 0 0 bp 0.00 %
LTR elements: 0 0 bp 0.00 %
ERVL 0 0 bp 0.00 %
ERVL-MaLRs 0 0 bp 0.00 %
ERV_classI 0 0 bp 0.00 %
ERV_classII 0 0 bp 0.00 %
DNA elements: 0 0 bp 0.00 %
hAT-Charlie 0 0 bp 0.00 %
TcMar-Tigger 0 0 bp 0.00 %
Unclassified: 0 0 bp 0.00 %
Total interspersed repeats: 0 bp 0.00 %
Small RNA: 0 0 bp 0.00 %
Satellites: 1 267 bp 0.00 %
Simple repeats: 663679 27953718 bp 1.39 %
Low complexity: 123705 6154714 bp 0.31 %
any idea or suggestions can help me out, please tq
favorite
I have been trying to detect, classify the transposable element in my eukaryotic non-referenced genome, (denovo)
I'm using RepeatMasker to do the job but whenever I run the tools the results shows only simple repeat and satellites.
where I'm trying to detect LTR elements, LINEs, SINES
bases masked: 33282890 bp ( 1.66 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
SINEs: 0 0 bp 0.00 %
Alu/B1 0 0 bp 0.00 %
MIRs 0 0 bp 0.00 %
LINEs: 0 0 bp 0.00 %
LINE1 0 0 bp 0.00 %
LINE2 0 0 bp 0.00 %
L3/CR1 0 0 bp 0.00 %
RTE 0 0 bp 0.00 %
LTR elements: 0 0 bp 0.00 %
ERVL 0 0 bp 0.00 %
ERVL-MaLRs 0 0 bp 0.00 %
ERV_classI 0 0 bp 0.00 %
ERV_classII 0 0 bp 0.00 %
DNA elements: 0 0 bp 0.00 %
hAT-Charlie 0 0 bp 0.00 %
TcMar-Tigger 0 0 bp 0.00 %
Unclassified: 0 0 bp 0.00 %
Total interspersed repeats: 0 bp 0.00 %
Small RNA: 0 0 bp 0.00 %
Satellites: 1 267 bp 0.00 %
Simple repeats: 663679 27953718 bp 1.39 %
Low complexity: 123705 6154714 bp 0.31 %
any idea or suggestions can help me out, please tq
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