其中代码里的-bc的意思是使用bias矫正信号(目前只支持ATAC-seq数据)。-nc是cpu数量: #这一行代码是教程里的原代码 $ rgt-hint differential --organism=mm9 --bc --nc 30 --mpbs-files=./match/cDC1_mpbs.bed,./match/pDC_mpbs.bed --reads-files=cDC1.bam,pDC.bam --conditions=cDC1,pDC --outp...
此外,通过比较两个ATAC-seq文件(cDC1细胞和pDC细胞),我们可以了解两个细胞中TF结合的变化。 下面这行代码将读取上面第四步里生成的motif 匹配文件和原始的bam文件。其中代码里的-bc的意思是使用bias矫正信号(目前只支持ATAC-seq数据)。-nc是cpu数量: #这一行代码是教程里的原代码$ rgt-hint differential--organis...
Monocle2包学习笔记(四):Differential Expression Analysis Palantir包学习笔记 使用Palantir进行单细胞发育轨迹推断分析 Signac包学习笔记 使用Signac包进行单细胞ATAC-seq数据分析(一):Analyzing PBMC scATAC-seq 使用Signac包进行单细胞ATAC-seq数据分析(二):Motif analysis with Signac 使用Signac包进行单细胞ATAC-seq数据...
Tutorial Three: In this section we will focus on differential peak identification, motif footprinting, and annotation of nearby genomic features. Workflow for sc-ATAC Sequencing (submodule 4). Tutorial Four: In this section we will demonstrate a single cell ATAC-Seq analysis workflow. GCP Architectu...
Differential accessibility analysis, PCA and clustering (R, DESeq2) Create IGV session file containing bigWig tracks, peaks and differential sites for data visualisation (IGV). Present QC for raw read, alignment, peak-calling and differential accessibility results (ataqv, MultiQC, R) Quick Start ...
Cell Ranger ATAC cannot perform differential analysis for transcription factor motifs in the cases where the motifs.pfm file is missing from the reference package, such as in custom references built without the motif file or in multi-species experiments. Cell Ranger ATAC will always perform different...
conquer- A repository of consistently processed, analysis-ready single-cell RNA-seq data sets. D3E- Discrete Distributional Differential Expression (D3E) is a tool for identifying differentially-expressed genes, based on single-cell RNA-seq data. ...
analysis, and specifically the integration of data from different sources. We have developed a dedicated computational approach: a variational auto-encoder using a noise model specifically designed for single-cell ATAC-seq (assay for transposase-accessible chromatin with high-throughput sequencing) data,...
Tutorial for the use of HINT-ATAC with the hematopoietic data set is provided in https://www.regulatory-genomics.org/hint/tutorial-differential-footprints-on-scatac-seq/. References Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of ...
Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly u