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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 3 months ago

shehongbing commented 6 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 6 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.