SPatacseq

🚧 Under Development!

This pipeline is currently under development and does not have a stable release yet.

Installation

To install the package, please use the BiocManager::install command:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("systemPipeR/SPatacseq", build_vignettes=TRUE, dependencies=TRUE)

To obtain the systemPipeR and systemPipeRdata, please run as follow:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("systemPipeR")
BiocManager::install("systemPipeRdata")

Usage

Pipeline summary

  • Read Preprocessing
    • Preprocessing with preprocessReads function
    • Preprocessing with TrimGalore!
    • Preprocessing with Trimmomatic
  • FASTQ quality report
  • Alignment against reference genome
    • Alignment with Bowtie2
    • Alignment with BWA
  • Create symbolic links for viewing BAM files in IGV
  • Peak calling with MACS2
  • Annotate peaks
    • Annotation with ChIPpeakAnno package
    • Annotation with ChIPseeker package
  • Count reads overlapping peaks
  • Differential binding analysis
  • GO term enrichment analysis
  • Motif analysis
    • Motif discovery with BCRANK