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zhangrengang / Centromics

Centromics: visualing centromeres with multiple omics data
GNU General Public License v3.0
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how to analyse the Centromics result #11

Open cell-c opened 11 months ago

cell-c commented 11 months ago

hi, thank you so much for this tool for identifying the centromere. I have run this tool with our long reads and HiC reads. I would like to ask for help in terms of the Centromics result and how to find the centromere sequences. Many thanks.

centomics.trf.fa centomics.trf.count centomics.hic.count.100000.intra_chr centomics.hic.count.100000.inter_chr centomics.candidate_peaks.bed centomics.circos.png centomics.circos centomics.circos.pdf centomics.circos_legend.pdf centomics.circos_legend.txt

zhangrengang commented 11 months ago

Hi. You may firstly check the figures (*.pdf) and find the putative centromere. Then the tandem sequences can be found in centomics.trf.fa.

Threeman8 commented 9 months ago

@zhangrengang 哈喽，首先非常感谢您的软件！非常有帮助，谢谢！ 想请教3个问题： 1.结果中的circos.pdf的内圈hic信号是怎么解读的呢？ 2.在我的结果中，是否可以认为chr4的着丝粒区域是40-60MB之间的那个串联重复呢？ 3.如何引用您的工作？ 非常感谢！

下图是我的结果： image

zhangrengang commented 9 months ago
  1. hic的高峰处可能是着丝粒区域，但这个不是所有物种都如此。
  2. 我觉得可能是chr5 40Mb那个位置的串联重复吧。
  3. 尚未发表，可暂且引用github链接。
Blosers commented 6 months ago

您好，非常感谢您提供这个用于识别着丝粒的工具。我已经用我们的长读和 HiC 读运行了这个工具。我想就 Centomics 结果以及如何找到着丝粒序列寻求帮助。非常感谢。

centomics.trf.fa centomics.trf.count centomics.hic.count.100000.intra_chr centomics.hic.count.100000.inter_chr centomics.candidate_peaks.bed centomics.circos.png centomics.circos centomics.circos.pdf centomics.circos_legend. pdf centomics.circos_legend.txt

您好，你是怎么确定着丝粒的位置的，我看了我的circos 图片还是没有办法确定到底哪里是着丝粒。