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aaranyue / quarTeT

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification
http://atcgn.com:8080/quarTeT/home.html
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What sequence should I use to visualise the centromere #29

Closed shehongbing closed 7 months ago

shehongbing commented 10 months ago

Hi, Thanks for your powerful tool. I have a question about the Centromere module.

I get the best candidate centromeres, as follows (using Chr4 as an example, the Chr4 with a centromere of 65 Mb-66 Mb),

Chr4    65897059        66008690        111632  11816   10.58%  98649   88.37%  0.19421934767224158
Chr4@TR_03018   200     1338    1.2%
Chr4@TR_00285   183     1070    0.96%
Chr4@TR_01112   167     1060    0.95%
Chr4@TR_00608   166     953     0.85%
Chr4@TR_00650   130     757     0.68%
...

Then, I extracted all of above TR from the GFF3 file (TRgff3/*Chr4.tr.blast.gff3) and visualised it in IVG, however, I cannot obtain corresponding centromere at 65 Mb-66 Mb (see below). image

Thus, What sequence should I use to visualise the centromere.

Thx Hongbing

Echoring commented 10 months ago

Right click and select Expanded mode, and enlarge the viewing region focus on the candidate region may be of help. Meanwhile, the best candidate is just a prediction. It's highly recommended to check other candidates, and combine TR, TE, and gene content, Hi-C heatmap, pairwise colinearity etc. to vote your candidates. Only one evidence is not enough to locate the centromere in complex genome.