Is it necessary for --anno 1 for pangenome in the initial annotation?

[jia-wu-feng]

https://github.com/HuffordLab/NAM-genomes/tree/master/te-annotation

Generate de novo TE library for each genome and perform initial annotation.

Is it necessary for --anno 1 for this step?

[oushujun]

Hi, yes it's necessary. You will need to use this initial annotation to screen for TE candidates to generate the pan-genome library.

[jia-wu-feng]

Hi shujun,

When closed --anno, I also got the library in *.mod.EDTA.final I don't have --curatedlib, so I just use this software results.

for *.EDTA.TElib.fa, is it different?

Thanks.

[oushujun]

Hi Jia-Wu,

Not sure I follow your question. You do not need to provide --curadedlib, but when you provide curated TE sequences, it will improve the annotation and also harness previous work.

Shujun

[jia-wu-feng]

Hi, shujun,

I am sorry for my expression.

My command: EDTA.pl --genome FB19_011_3_pseudomolecules_v6_hap1.fasta.1.contig.fa -t 28 --cds HBULBOSUM.r1.pgsb.Dec2021.high.cds.fa --anno 1

The results of EDTA

When I don't use --curatedlib, EDTA doesn't generate the file $genome.mod.EDTA.TElib.novel.fa.

In the pangenome pipeline, I use FB19_011_3_pseudomolecules_v6_hap1.fasta.1.contig.fa.mod.EDTA.TElib.fa file to do next step. Is it right?

When I use --anno 0, I think it also generate the file FB19_011_3_pseudomolecules_v6_hap1.fasta.1.contig.fa.mod.EDTA.TElib.fa.

Do you think FB19_011_3_pseudomolecules_v6_hap1.fasta.1.contig.fa.mod.EDTA.TElib.fa is same.

I think if I use --anno 0, I can save time in the first step. Is it right?

Thanks.

[oushujun]

hello,

Sorry for missing this thread. -anno 1 is required because the initial annotation is needed for filtering of individual libraries.

Thanks, Shujun