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oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
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Overlapping TEs #401

Closed bijendrabio closed 5 months ago

bijendrabio commented 7 months ago

@oushujun Curious if EDTA double counts bp sizes for different overlapped TEs while generating the summary of whole-genome TE annotation (genome.mod.EDTA.TEanno.sum)

For example, overlapped TEs (structurally intact and fragmented TEs) in genome.mod.EDTA.TEanno.gff3 file: EDTA

Regards, B

oushujun commented 7 months ago

Hi,

The summary is generated by /EDTA/util/buildSummary.pl adapted from RepeatMasker. It handles over counting in some level but cases like yours I haven’t checked myself. Maybe you can extract just these fragments and resummrize with the script to check it out.

Thanks, Shujun

On Fri, Nov 10, 2023 at 3:57 PM bijendrabio @.***> wrote:

@oushujun https://github.com/oushujun Curious if EDTA double counts bp sizes for overlapped TEs while generating the summary of whole-genome TE annotation (genome.mod.EDTA.TEanno.sum)

For example, overlapped TEs (structurally intact and fragmented TEs) genome.mod.EDTA.TEanno.gff3, [image: EDTA] https://user-images.githubusercontent.com/98179638/282176746-dbfbdb26-103b-4562-9a58-b646adb96d40.PNG

Regards, B

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