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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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Why the sequence masked in “.mod.masked” is greater in number than that in "mod.MAKER.masked"? #353

Closed lpzoaa closed 1 year ago

lpzoaa commented 1 year ago

Hi, shujun. Thank you for creating such a useful tool，and I have finished my TE annotation by EDTA.

I still have some questions and wanna consult with you. I found the sequence masked in “.mod.masked” file is greater in number than that in ".mod.MAKER.masked" file ( N count in “.mod.masked” =43051401; N count in ".mod.MAKER.masked"=22361329), and I also masked the sequence manually according to the “.mod.EDTA.TEanno.gff3” file by bedtools, which result was similar with ".mod.MAKER.masked" file but not necessarily identical (N count in ".mod.masked"=43051401; N count in masked manually based on ".mod.EDTA.TEanno.gff3” =42185967). Which file should be used in gene annotation?

oushujun commented 1 year ago

Please read the program status output, the user manual, the wiki, or other user issues. You can find the answer in many places :)

Edit: The wiki does not have a particular answer for this question, but contains many useful information.