zhuang_gj
3月-11-2021
上一次分析讲了如何整理好Copy Number Segment 数据,这次我们使用GISTIC2.0来识别体细胞拷贝数改变(SCNA),然后找到这些拷贝数显著变化的多基因区域。
- GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
- Gistic2.0 软件
- Copy Number Variation Analysis Pipeline
数据准备
- seg file:MaskedCopyNumberSegment(Tumor).txt
- markers file:hg_marker_file.txt
- refgene file:在线分析提供参考基因组
Gistic官网
image.png这三个文件必须要准备才能进行分析。点击Upload file 上次相关文件。参考基于组选择的是Hg38
image.png选择性调整参数.
image.png这里我设置的是0.99
点击RUN
运行完成后是这样的
image.png
总共是19个文件。
得到结果后就是理解输出结果的内容。
Gistic 2.0输出结果解释
- all_lesions.conf_XX.txt,其中XX是置信度
汇总了GISTIC运行的结果。它包含有关扩增和缺失重要区域的数据,以及每个区域中扩增或缺失哪些样品的数据。
- 扩增基因文件(Amp_genes.conf_XX.txt,其中XX是置信度)
- 缺失基因文件(Del_genes.conf_XX.txt,其中XX是置信度)
- all_thresholded.by_genes.txt
The table in this file is obtained by applying both low- and high-level thresholds to the gene copy levels of all the samples. The entries with value +/- 2 exceed the high-level thresholds for amps/dels, and those with +/- 1 exceed the low-level thresholds but not the high-level thresholds. The low-level thresholds are just the 'amplifications_threshold' and 'deletions_threshold' noise threshold input values (typically 0.1 or 0.3) and are the same for every threshold.
Amplification GISTIC plot:
上面是G-scores ,下面是q-values ,显示每条染色体显著扩增的位置。在“绿色”垂线右边的是有统计学意义的。同理可得Deletion GISTIC plot。
amp_qplot.png del_qplot.png下次分享maftools可视化相关结果以及挑选拷贝数变化的基因。
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