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Immortal2333 / Telomeres_and_Centromeres

This is a method to find telomeres and centromeres in plants.
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the result of grep 'MULE-MuDR' is empty #4

Closed MuyuenHoshino closed 1 year ago

MuyuenHoshino commented 1 year ago

Dear Immortal2333, I runned EDTA and get genome.mod.EDTA.TEanno.gff3.And then I use grep to extract keywords.I got results of Copia, Gypsy, Helitron correctly but when I use grep 'MULE-MuDR' genome.mod.EDTA.TEanno.gff3 > TE_MULE-MuDR.split.gff3,I got an empty file.And there is also nothing about MULE-MuDR in genome.mod.EDTA.TEanno.gff3. 2311687008539_ pic This is the sum of TE annoation.It's the same as this plot in your paper. image So which part is the MULE-MuDR? What am I doing wrong? Hope to get your help.(By the way,may i know how you drew this line chart?) Best wishes

Immortal2333 commented 1 year ago

We actually used the improved TE Annotation (66.47%) instead of EDTA to extract different types of TEs, because EDTA only annotated around 46% in the Vitis genus. Perhaps you can consider using this Pan-genome TE Annotation Pipeline to enhance your results of TE detection. The pipeline I shared serves as an example to demonstrate how we can identify centromeres through TRF, TE, and Gene annotations. Additionally, EDTA can also be used for centromere identification (Copia, Gypsy, and Helitron are acceptable).

PanTE classified

MuyuenHoshino commented 1 year ago

Dear Immortal2333, Thanks for your prompt reply,and sorry for not being on github these days You are so generous in sharing knowledge Best wishes