Closed hkchi closed 4 years ago
Sorry I realized this might be duplicate of #8 and #58. I suppose that the LINE/SINE will need to be picked up by RepeatModeler/RepeatMasker in the FINAL step for animal genomes.
We benchmarked SINE/LINE search programs in the paper using the rice genome. The performance was not satisfactory, so none of these tools were used in the EDTA pipeline. However, I didn't benchmark these tools using any animal genomes (ie. human), so I don't know whether these tools are just poor in rice or also in other genomes.
Hi Shujun,
It seems that EDTA does not specifically identify LINE/SINE since EDTA_raw.pl only finds ltr|tir|helitron. Has it been benchmarked in animal genomes (e.g. human) where these elements are more prevalent?
Thanks, Kaichi