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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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TIR filtration #426

Closed bijendrabio closed 3 months ago

bijendrabio commented 4 months ago

Hello Shujun, Curious if the TIR elements identified using "EDTA_raw.pl --type tir" requires filtering. Its generate two files .intact.fa and .raw.fa, both of which are same. Does this indicate that additional processing is needed?

Regards, B

oushujun commented 4 months ago

It's already filtered by EDTA_raw and produced the two files. And yes, they are identical just for programmatic convenience. They will be further filtered by EDTA_processK.pl in the .combine folder.

Shujun

bijendrabio commented 4 months ago

Thanks @oushujun. So does the initial filtered file need to be filtered further using EDTA_processK.pl? I only want to annotate TIR elements? or Can I just use RepeatMasker using the initial output to annotate TIR?

oushujun commented 4 months ago

Process_K will get more false positive filtered, but the intact file in raw is already heavily filtered. It’s your call.

Shujun

On Thu, Feb 1, 2024 at 12:21 PM bijendrabio @.***> wrote:

Thanks @oushujun https://github.com/oushujun. So does the initial filtered file need to be filtered further using EDTA_processK.pl? I only want to annotate TIR elements? or Can I just use RepeatMasker using the initial output to annotate TIR?

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