zhangrengang

I do not understand. Are you using `-genome` option to screen a whole genome with TEsorter? Otherwise, you should not input genome fasta, but input TE fasta identified by e.g....

You are right. Please note that the `-genome` option do not produce a TE library like RepeatModeler, but output annotations (`*.dom.gff3`) and sequences (`*.dom.faa`) of TE protein domains across the...

It is strange. How did you install it? Is it the last version from github?

I test the conda version, but only four files output: ``` $ TEsorter -genome rice6.9.5.liban -fw $ ls rice6.9.5.liban.rexdb.domtbl rice6.9.5.liban.rexdb.dom.gff3 rice6.9.5.liban.rexdb.dom.faa rice6.9.5.liban.rexdb.dom.tsv ```

Yes.

It works. It is fast for small TE library.

You may use the union set of non-unknown TEs from RepatModeler and TEsorter.

I mean you may replace the unknown classifications by TEsorter with the known classifications by RepeatModeler, like: ``` less rice6.9.5.liban.rexdb.cls.lib | awk '{if ($1~"#Unknown"){cls=$1; $1=">"$2; $2=cls}{print}}' ``` It is just...

Hi. It is true for some species, such as Brassica napus (9 and 10 chromosomes). Please show me your plots (at least the heatmap and circos plots) to have a...

LG21 seems to be incorrectly assigned, meaning that each subgenome should have 12 chromsomes. I suggest you reduce the `-q` to 50 or 100 to obtain more differentail kmers.