Unclear about raw and TE fasta files

[katieemelianova]

Hi there,

I wanted to clarify the status of an output file in the .final folder of EDTA, I have a file titled

species.fasta.mod.EDTA.final/species.fasta.mod.EDTA.raw.fa

From the schematic in Figure 1. of "A Tutorial of EDTA: Extensive De Novo TE Annotator" it seems as though raw files have not gone through CDS filtering, however this file is in the .final folder - is this just a copy of the output from the .raw folder? My aim is to get a fasta file of intact, full length and fragmented TEs which have gone through EDTA and CDS filters. I thought perhaps that the file that I would need might be:

species.fasta.mod.EDTA.anno/species.fasta.mod.EDTA.TE.fa

But I could not yet figure out what this file is. Could you clarify what these two files are please? Any advice would be greatly appreciated :)

Best,

Katie

[oushujun]

Hi Katie,

You are correct, the raw.fa file has been copied to different folders. You should use the final TEanno.gff3 file to extract intact and fragmented TEs.

THanks!
Shujun