I am using EDTA+panEDTA to annotate genomes of 40 related species. I annotated each genome individually with EDTA v2.2.0 and generated a panEDTA library. Then for each genome, I run
These are copy-paste from panEDTA.sh for parallization.
In my understanding, each sequence in the panEDTA TE library should represent a TE family. I am trying to extract genomic sequences for each TE family. I found some unusual Names in attributes field of TEanno.gff3:
(1) There are some panTE_XXX in gff3 but not in panEDTA.TElib. Instead, there are panTE_XXX_INT and panTE_XXX_LTR in panEDTA.TElib.
(2) There are TE_XXX in gff3, but not in panEDTA.TElib.
Lastly, how would you count the copy number of each TE family? I checked the ratio between length of regions in the gff3 and of corresponding sequences in panEDTA.TElib, and it differs a lot. Here are quantiles of the ratio:
I suspect whether these extremely short/long regions are really transposons and I am not sure whether it is a good idea to include them in analysis analysis on evolution of individual TE family (e.g. copy number dynamics). Do you have any suggestion?
Hello,
I am using EDTA+panEDTA to annotate genomes of 40 related species. I annotated each genome individually with EDTA v2.2.0 and generated a panEDTA library. Then for each genome, I run
These are copy-paste from
panEDTA.sh
for parallization.In my understanding, each sequence in the panEDTA TE library should represent a TE family. I am trying to extract genomic sequences for each TE family. I found some unusual
Names
in attributes field of TEanno.gff3: (1) There are some panTE_XXX in gff3 but not in panEDTA.TElib. Instead, there are panTE_XXX_INT and panTE_XXX_LTR in panEDTA.TElib. (2) There are TE_XXX in gff3, but not in panEDTA.TElib.Lastly, how would you count the copy number of each TE family? I checked the ratio between length of regions in the gff3 and of corresponding sequences in panEDTA.TElib, and it differs a lot. Here are quantiles of the ratio:
I suspect whether these extremely short/long regions are really transposons and I am not sure whether it is a good idea to include them in analysis analysis on evolution of individual TE family (e.g. copy number dynamics). Do you have any suggestion?
Sincerely,
Cong