oushujun
commented
4 months ago Hi Andre,
Thank you for using EDTA and panEDTA! Yes you are correct, that the library is just a representation of high-confident TE sequences. You may check out the TEanno.sum file of each genome which contains the presence of each family and their size. Many codes in the panEDTA GitHub is parsing that file type. You may also find information helpful in the EDTA wiki page.
Best, Shujun
On Wed, Feb 21, 2024 at 3:53 AM adeoliveira86 @.***> wrote:
Dear @oushujun https://github.com/oushujun,
I would like to thank you for the great tool. I have been using EDTA to annotate highly repetitive metazoan genomes and I am really happy with the results. I am finishing running panEDTA and I would like to obtain some insights into the evolution of the repeat families across my selected animal targets, similar to the analyses you described in your pre-print https://www.biorxiv.org/content/10.1101/2022.10.09.511471v1.
One detail which I am still struggling to link with traditional pangenome analyses is what elements in the panEDTA library are present in in all species, and which ones are only present in few (shell) or within single individuals (cloud). Based on the publication, it looks like to me that the "panEDTA" library file, cannot be interpreted as a traditional pangenome analysis outcome, because panEDTA actually filters and removes repeat elements identified in the different species (as described in the section below) following some criteria. This decreases the total number of elements which theoretically would be found with the union of all individual EDTA repeat libraries. Coming back to my analogy, the panEDTA library is most likely the representation of the "core" in a traditional pangenome pipeline. Is my interpretation correct?
I am asking this because I would like to add some evolutionary perspective into my analyses and trace back how the repeat families evolved across the lineage I am interested and how this impacted these animal's genome evolution. Is this possible to be done with the panEDTA results? I checked the git page associated with your publication and it is incredibly rich (git clone https://github.com/oushujun/PopTEvo.git) with many distinct scripts. Most likely one of those could be used to help achieving my goals.
Again thanks again for the incredible tool, Best, André
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adeoliveira86
Dear @oushujun,
I would like to thank you for the great tool. I have been using EDTA to annotate highly repetitive metazoan genomes and I am really happy with the results. I am finishing running panEDTA and I would like to obtain some insights into the evolution of the repeat families across my selected animal targets, similar to the analyses you described in your pre-print https://www.biorxiv.org/content/10.1101/2022.10.09.511471v1.
One detail which I am still struggling to link with traditional pangenome analyses is what elements in the panEDTA library are present in in all species, and which ones are only present in few (shell) or within single individuals (cloud). Based on the publication, it looks like to me that the "panEDTA" library file, cannot be interpreted as a traditional pangenome analysis outcome, because panEDTA actually filters and removes repeat elements identified in the different species (as described in the section below) following some criteria. This decreases the total number of elements which theoretically would be found with the union of all individual EDTA repeat libraries. Coming back to my analogy, the panEDTA library is most likely the representation of the "core" in a traditional pangenome pipeline. Is my interpretation correct?
I am asking this because I would like to add some evolutionary perspective into my analyses and trace back how the repeat families evolved across the lineage I am interested and how this impacted these animal's genome evolution. Is this possible to be done with the panEDTA results? I checked the git page associated with your publication and it is incredibly rich (git clone https://github.com/oushujun/PopTEvo.git) with many distinct scripts. Most likely one of those could be used to help achieving my goals.
Again thanks again for the incredible tool, Best, André