Software tools for Hi-C data analysis Hi-C可视化 image.png 数据分析 序列过滤 过滤原理 数据矫正 为什么要做数据矫正? Eitan Yaffe & Amos Tanay;2011 数据矫正效果 可做的分析 1.cis/trans互作比例 2.互作频率与距离有关 3.compartment分析 4.TAD分析 5.显著互作分析 image.png Hi-C的应用 1.解析全基因...
/data/training/zengjianming/biosoft/hicpro/bin/HiC-Pro_2.10.0/HiC-Pro/bin/HiC-Pro --help 然后我们这一讲的重点是Hic-pro软件的使用。 如果仅仅是看软件的帮助文档,会发现其实非常容易使用; usage : HiC-Pro -i INPUT -o OUTPUT -c CONFIG [-s ANALYSIS_STEP] [-p] [-h] [-v] ...
/data/training/zengjianming/biosoft/hicpro/bin/HiC-Pro_2.10.0/HiC-Pro/bin/HiC-Pro --help 然后我们这一讲的重点是Hic-pro软件的使用。 如果仅仅是看软件的帮助文档,会发现其实非常容易使用; usage : HiC-Pro -i INPUT -o OUTPUT -c CONFIG [-s ANALYSIS_STEP] [-p] [-h] [-v] -i|--input ...
复制 [-s|--stepANALYSIS_STEP]:run only a subsetofthe HiC-Pro workflow;ifnot specified the complete workflow is runmapping:perform reads alignment-require fast filesproc_hic:perform Hi-Cfiltering-requireBAMfilesquality_checks:run Hi-Cquality control plotsmerge_persample:merge multiple inputs and ...
HiC-bench: comprehensive and 485 reproducible Hi-C data analysis designed for parameter exploration and benchmarking. BMC 486 Genomics. 2017;18:22. doi:10.1186/s12864-016-3387-6.Lazaris C, Kelly S, Ntziachristos P, et al. HiC-bench: comprehensive and reproducible Hi-C data analysis ...
4D Nucleome Data Coordination and Integration Center and the Center for 3D Structure and Physics of the Genome hosted a Hi-C data analysis bootcamp at Harvard Medical School on May, 8th 2018. This repo contains the material for this bootcamp. Below, you can find more information on how to ...
HiC-Pro -i INPUT -o OUTPUT -c CONFIG [-s ANALYSIS_STEP] [options] -c: config文件路径 -o: 结果生成路径 -i: 原始数据路径 -p: 集群运行 5.结果解读 总目录 bowtie_results:比对结果目录 hic_results:hic矩阵及分析结果目录 logs:存放分析日志 ...
/data/training/zengjianming/biosoft/hicpro/bin/HiC-Pro_2.10.0/HiC-Pro/bin/HiC-Pro --help 然后我们这一讲的重点是Hic-pro软件的使用。如果仅仅是看软件的帮助文档,会发现其实非常容易使用;usage : HiC-Pro -i INPUT -o OUTPUT -c CONFIG [-s ANALYSIS_STEP] [-p] [-h] [-v] -i|--input ...
HiC互作矩阵文件: /PATH_to_analysis/HiC_data_out/hic_results/matrix/Lib/iced/1000000/L2_1000000_iced.matrix 文件具体内容如下:(每个数字代表的每个100Kb的区间,和bed文件对应)。 the matrix file is a three column sparse format in whichfirst two columns are interacting binsandthird column is interact...
nf-core-hic is a bioinformatics best-practice analysis pipeline for Hi-C/Capture-C data analysis. This pipeline is optimal for large scale analysis in High Performance Computing Clusters (HPCs) and Cloud Computing environments (eg. AWS). Also, it can be executed in hybrid environments (eg. ...