pseudo_omic_features_analysis_pipeline

This repository processes the pseudo-omic features induced by the extended S phase in cell composition.

Getting started

The workflow is described in the Figure folder. The Figure 1 section corresponds to the methods of WGS-related processes, such as the pipeline of WGS data, simulation S phase ratio, CNV segment calling, and visualization... The Figure 2 section corresponds to the methods of NicE-seq data analysis. The Figure 3 section corresponds to the methods of the DNA methylation data analysis. The Figure 4-5 section corresponds to the methods of the single-cell RNA-seq analysis. For details, see the documentation of each of the scripts below the folder.

Dependencies

You will need the following software: TrimGalore v0.6.3, BWA v0.7.17, DNAcopy v1.58.0, STAR v2.7.1a, featureCounts v1.6.4, MAST v1.10.0, MACS2 v2.1.1, sva v3.35.2

References

1. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013, 29(1): 15-21.
2. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 2013, 30(7): 923-930.
3. Krueger F. Trim Galore: a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. URL http://www bioinformatics babraham ac uk/projects/trim_galore/(Date of access: 28/04/2016) 2012.
4. McCarthy DJ, Campbell KR, Lun AT, Wills QF. Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics 2017, 33(8): 1179-1186.
5. McDavid A, Finak G, Yajima M. MAST: model-based analysis of single cell transcriptomics. R package version 0931 2015.
6. Seshan VE, Olshen AB. DNAcopy: a package for analyzing DNA copy data. Bioconductor Vignette 2014: 1-7.
7. Weddington N, Stuy A, Hiratani I, Ryba T, Yokochi T, Gilbert DM. ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data. BMC bioinformatics 2008, 9(1): 530.