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View Code? Open in Web Editor NEWBioinformatics-pipeline in snakemake.
Bioinformatics-pipeline in snakemake.
snakemake workflows ref:https://github.com/snakemake-workflows 1. project list ATAC-seq/ demo1: for replicate samples; ATAC-seq/ demo2: for plate method, 1 by 1 map, then merge. change from BWA to bowtie2; R_script/ demo1: how to run parallel using snakemake in R environment, and wait for a file to generate. 2. How to run (1) -n 模拟运行: 检查语法错误 $ snakemake -np -s /data/wangjl/soft/snakemakeWorkflow/R_script/demo1/main.sf -j 4 -p 打印正在运行的命令。 -j 4 使用线程数 (2) 画流程图: 总体是否符合逻辑 步骤流程图 $ snakemake -f -s s1.sf --rulegraph 2> /dev/null | dot -T pdf > workflow.pdf 样本流程图 $ snakemake --dag -s s1.sf | dot -Tpdf > dag.pdf 加 -forceall 则强制全部重新运行一次。 (3) 实际运行命令 $ snakemake -s /data/wangjl/soft/snakemakeWorkflow/R_script/demo1/main.sf -j 4
https://pubmed.ncbi.nlm.nih.gov/22908215/
https://academic.oup.com/bioinformatics/article/28/19/2520/290322
https://f1000research.com/articles/10-33/v2
Code style:
(a) workflow definition; hypothesized knowledge requirement for line readability is color-coded on the left next to the line numbers.
(b) directed acyclic graph (DAG) of jobs, representing the automatically derived execution plan from the example workflow; job node colors reflect rule colors in the workflow definition.
(c) content of script plot-hist.py referred from rule plot_histogram.
(d) knowledge requirements for readability by statement category (see subsection 3.3).
The example workflow downloads data, plots histograms of city populations within a given list of countries, and converts these from SVG to PDF format. Note that this is solely meant as a short yet comprehensive demonstration of the Snakemake syntax.
Single or multiple external workflows can be declared as modules, along with the selection of all or specific rules. Properties of rules can be overwritten, and the analysis can be extended with further rules.
For brevity only rule properties that are necessary to understand each example are shown (e.g. omitting log directives and shell commands or script directives).
(a) scatter/gather process,
(b) streaming,
(c) non-file parameters,
(d) iteration,
(e) sample sheet based configuration,
(f) conditional execution,
(g) benchmarking,
(h) parameter space exploration. See subsection 3.2 for details.
https://www.nature.com/articles/nmeth.2688
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
表观测序领域大牛William J Greenleaf和Howard Y Chang的经典之作,引用上千次的ATAC经典原文
https://yiweiniu.github.io/blog/2019/03/ATAC-seq-data-analysis-from-FASTQ-to-peaks/
https://pubmed.ncbi.nlm.nih.gov/32014034/ From reads to insight: a hitchhiker's guide to ATAC-seq data analysis
其他的工具 macs,bowtie,igv 有对应的官网,也有网友写的中文博客
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