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how to analyse the Centromics result #11

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cell-c opened this issue Oct 6, 2023 · 4 comments
Open

how to analyse the Centromics result #11

cell-c opened this issue Oct 6, 2023 · 4 comments

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@cell-c
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cell-c commented Oct 6, 2023

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
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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
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@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
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  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
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Blosers commented Mar 18, 2024

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。

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