标签：file GenomeDISCO contact samples bins metadata
评估从染色体捕获实验获得的一对接触图的相似性。GenomeDISCO设计用于评估从染色体构象捕获实验获得的染色质接触图的一致性和可重复性。它对测序深度，结点和边缘缺失噪声，结构域边界的变化以及距离依赖性的细微差别的识别灵敏度高，将生物重复与不同细胞类型区分开来。
GenomeDISCO (DIfferences between Smoothed COntact maps) is a package for comparing contact maps of 3D genome structures, obtained from experiments such as Hi-C, Capture-C, ChIA-PET, HiChip, etc. 在比较接触图之前，它使用接触图图上的随机行走进行平滑，从而产生一致性分数，可用于生物重复的质量控制。
比较两个接触图
1. 得到配置文件
/genomedisco/examples/configure_example.sh
2. 进行一致性分析
cd genomedisco genomedisco run_all --metadata_samples examples/metadata.samples --metadata_pairs examples/metadata.pairs --bins examples/Bins.w50000.bed.gz --outdir examples/output
Inputs
运行 GenomeDISCO 前，
要有以下文件
-
contact map For each of your samples, you need a file containing the counts assigned to each pair of bins in your contact map, and should have the format
chr1 bin1 chr2 bin2 value. Note: GenomeDISCO assumes that this file contains the contacts for all chromosomes, and will split it into individual files for each chromosome. -
bins This file contains the full set of genomic regions associated with your contact maps, in the format
chr start end namewhere name is the name of the bin as used in the contact map files above. GenomeDISCO supports both fixed-size bins and variable-sized bins (e.g. obtained by partitioning the genome into restriction fragments).
GenomeDISCO 需要下列输入文件:
-
--metadata_samples要比较的样本信息. Tab-delimited file, with columns "samplename", "samplefile". Note: each samplename should be unique. Each samplefile listed here should follow the format "chr1 bin1 chr2 bin2 value -
--metadata_pairs每一行是一对要比较的样本名。 in the format "samplename1 samplename2". Important: sample names used here need to correspond to the first column of the --metadata_samples file. -
--binsA (gzipped) 分析中用到的所有bins的bed file。 It should have 4 columns: "chr start end name", where the name of the bin corresponds to the bins used in the contact maps. -
--re_fragments 如果基因组中的bins不均一就加上flag (例如，如果它们是基于限制性内切酶的).默认情况下这些代码认为bins是均一的长度。 -
--parameters_file生物重复和QC分析的参数 For details see "Parameters file" -
--outdirName of output directory. DEFAULT: replicateQC -
--running_modeThe mode in which to run the analysis. This allows you to choose whether the analysis will be run as is, or submitted as a job through sge or slurm. Available options are: "NA" (default, no jobs are submitted). Coming soon: "sge", "slurm" -
--concise_analysisSet this flag to obtain a concise analysis, which means replicateQC is measured but plots that might be more time/memory consuming are not created. This is useful for quick testing or running large-scale analyses on hundreds of comparisons. -
--subset_chromosomesComma-delimited list of chromosomes for which you want to run the analysis.该参数选择部分染色体进行分析。 默认在所有染色体上进行分析。This is useful for quick testing
来源：
https://omictools.com/genomedisco-tool
https://github.com/kundajelab/genomedisco
标签：file,GenomeDISCO,contact,samples,bins,metadata 来源： https://www.cnblogs.com/bio-mary/p/12524878.html
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