search

Immortal2333 / Telomeres_and_Centromeres

This is a method to find telomeres and centromeres in plants.
36 stars 6 forks source link

the abnomal distribution of the gaspy elements, how could deal with it #1

Closed Jiangjiangzhang6 closed 1 year ago

Jiangjiangzhang6 commented 1 year ago

hello I use your method to identified the centromeres. but the igv is like this. e3bd77b7af9eda23980b305c4c7dc97 and the gaspy elements was abnormal, so I want to ask how could it emrge this error? And my genome was gap-free, assemblied main frame use th hifi data and gap-filling use the graph assemblied by clr data. the genome busco and protein busco were 99.8% and 96%, respectively. the LAI was 23, so I think the genome quality should be good. so this case was abnoml or not , how could i deal with it. thank you

Immortal2333 commented 1 year ago

It is a common phenomenon in most plants to identify the centromere region. To accomplish this, you can zoom in on the peak of the chromosome and combine it with TRF repeat units, utilizing IGV visualization. If you'd like, you can send the 'genome_trf.split.gff' file to my email at 571720850@qq.com. I will do my best to assist you in finding the TRF repeat units, provided I am available. Good luck with your endeavors!