Total length annotated by RepeatMasker is longer than LTR_retriever about ltr_retriever

[oushujun]

Hi th,

LTR_retriever identifies intact LTR elements and constructs a non-redundant library to annotated fragmented LTR sequences. By saying much shorter length, did you mean intact only or both intact and fragmented LTR sequences?

Shujun

[th2ch-g]

Dear, oushujun.

Thank you for replying.

I meant intact LTR only. I think that is why LTR annotated by LTR_retriever is much shorter.

By the way, I calculated annotated LTR from .pass.list(LTR_retriever output file) and .out(RepeatMasker output file).

Sincerely,
th

[oushujun]

Hello th,

LTR_retriever annotates whole-genome LTR sequences (intact and fragmented), which could be found in the .out.gff file. The .pass.list file only contains intact LTR elements. The .out(RepeatMasker output file) should contain all LTR sequences (intact and fragmented). So you should compare the LTR_retriever .out.gff file with the RepeatMasker .out file.

Best,
Shujun