ATAC-seq data analysis: from FASTQ to peaks Yiwei Niu,Last updated: 2019 Blog style walkthrough of generalized ATAC-seq data analysis. https://yiweiniu.github.io/blog/2019/03/ATAC-seq-data-analysis-from-FASTQ-to-peaks/ BIOINF525 Lab 3.2 Steve Parker,Last updated: 2016 Minimal standard ATAC...
ATAC-seq data analysis: from FASTQ to peaks Yiwei Niu,Last updated: 2019 Blog style walkthrough of generalized ATAC-seq data analysis. https://yiweiniu.github.io/blog/2019/03/ATAC-seq-data-analysis-from-FASTQ-to-peaks/ BIOINF525 Lab 3.2 Steve Parker,Last updated: 2016 Minimal standard ATAC...
trim_galore --cores 30 -q 20 --length 20 --max_n 3 --stringency 3 --fastqc --paired -o ./ ../rawdata/SRR14205836_1.fastq.gz ../rawdata/SRR14205836_2.fastq.gz trim_galore --cores 30 -q 20 --length 20 --max_n...
网址:https://yiweiniu.github.io/blog/2019/03/ATAC-seq-data-analysis-from-FASTQ-to-peaks/ 续接上一个帖子:一个优秀的ATAC-seq数据分析资源实战(一) 上次运行到使用Picard的MarkDuplicates工具去除PCR重复的reads时,这里报错: java -XX:ParallelG...
里面的全流程已经给大家介绍完了第一个:ATAC-seq data analysis: from FASTQ to peaks 一个优秀的ATAC-seq数据分析资源实战(一) 一个优秀的ATAC-seq数据分析资源实战(二) 今天来学习第二个:Analysis of ATAC-seq data in R and Bioconductor https://rockefelleruniversity.github.io/RU_ATACseq/ 这个教程主要...
imputed_data.txt: 每个细胞在每个特征的推断值,建议用--binary保存二进制格式 model.pt: 用于重复结果的模型文件,--pretrain参数能够读取该模型 feature.txt: 每个细胞的隐特征,用于聚类和可视化 cluster_assignments.txt: 两列,barcode和所属类群 tsne.txt, tsne.pdf: tSNE的坐标和PDF文件,坐标文件可以导入到R语...
Loading data from a simple sparse matrix format 一般的散点矩阵加载数据,例子给出的是来自Mouse sci-ATAC-seq Atlas肾脏数据的示例数据集。 library(cicero) library(monocle3) # Code to download (54M) and unzip the file - can take a couple minutes ...
我们将使用 Hao 等人(2020年)的注释 PBMC 参考数据集,可以从这里下载:https://atlas.fredhutch.org/data/nygc/multimodal/pbmc_multimo... 请注意,加载参考数据集需要安装 SeuratDisk 包。 library(SeuratDisk) # load PBMC reference reference <- LoadH5Seurat("../vignette_data/multiomic/pbmc_multimodal.h5...
文章标题:Comparison of differential accessibility analysis strategies forATAC-seqdata 发表期刊:Scientific Reports 影响因子:3.998 (2019) 研究背景 哺乳动物基因组中的基因调控涉及到不同类型的调控原件,诸如启动子、增强子和绝缘子。据估计在人类和小鼠基因组中有超过两百万调控原件,并且这些调控原件涉及不同的表观...
ATAC-Seq data from experiments performed with the ATAC-Seq Kit correlates very well with published ATAC-Seq data, highlighting that this assay is robust and reproducible. Figure 2: ATAC-Seq Kit Libraries Correlation with Published ATAC-Seq Dataset. Here, the correlation between RPKM signal in ...