LINE1 reference, LINE1 subfamily and LINE1 structure

[Tesdhi]

Hello @simoncchu,

I am using xTea for to analyze LINE1 in my Nanopore direct DNA-seq data of human samples, Could I ask some questions?

1. The xTea uses "/home/ec2-user/rep_lib_annotation/consensus_mask_lrd/LINE1.fa" as the reference LINE1 consensus sequence for xtea_long analysis. Am I right?
2. In the xTea_long output file ("classified_results.txt.merged_LINE1.txt"), the "type" column only showed "LINE1", how could I identified the LINE1 subfamilies (like L1HS, L1PA2...)?
3. In the xTea_long output file ("classified_results.txt.merged_LINE1.txt"), the "structure" column showed "none", internal_inversion_deletion","internal_inversion" and "internal_deletion". Does the "none" means that they are "full-length L1" or "truncted L1"?
4. And are there any methods to directly distinguish the "full-length L1", "5' truncated L1" and "3' truncated L1" in the xTea_long output?

Many thanks for your kind help! Tesdhi