TIR filtration

[bijendrabio]

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]

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]

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]

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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