About repeat elements in the results of EDTA!

[sunnycqcn]

Hello,
I tried a small dataset and got the results as following:
Confusion matrix of BL06.R11.pilon.fasta.EDTA.TE.fa.stat for the all category
DNA/DTC DNA/DTH DNA/DTM LTR/Copia LTR/unknown MITE/DTM Misclas_rate
DNA/DTC 7 0 0 0 0 0 0.0000
DNA/DTH 0 1163 1 0 0 0 0.0009
DNA/DTM 0 0 7936 0 3 1 0.0005
LTR/Copia 0 0 0 259 0 0 0.0000
LTR/unknown 1 1 4 0 25193 1 0.0003
MITE/DTM 0 0 2 0 0 168 0.0118
So my question is that EDTA can analyze the repeat elments, such as AT-rich, GC-rich, short repeat elments, like (AT)n.
Thanks,
Fuyou

[oushujun]

Dear Fuyou,

You must be using a very standardized dataset. Your results are super good! The misclassification rate is even lower than the curated library (0.1%-2%).
To answer your question, no EDTA does not have the functionality to identify low complexity sequences or tandem repeats. You may use RepeatMasker to do so.

Best,
Shujun

[sunnycqcn]

Thanks.
Fuyou