Astrocyte ChIPseq analysis Workflow Package
This SOP describes the analysis pipeline of downstream analysis of ChIP-seq sequencing data. This pipeline includes (1) Quality control using Deeptools, (2) Peak annotation, (3) Differential peak analysis, and (4) motif analysis. BAM files and SORTED peak BED files selected as input. For each sample this workflow:
1) Annotate all peaks using ChipSeeker
2) Qulity control and signal profiling with Deeptools
3) Find differential expressed peaks using DiffBind
4) Annotate all differentially expressed peaks
5) Using MEME-ChIP in motif finding for both original peaks and differently expressed peaksAnnotations used in the pipeline
ChipSeeker - Known gene from Bioconductor [TxDb annotation](https://bioconductor.org/packages/release/BiocViews.html#___TxDb)
Deeptools - RefGene downloaded from UCSC Table browserWorkflow Parameters
bam - Choose all ChIP-seq alignment files for analysis.
genome - Choose a genomic reference (genome).
peaks - Choose all the peak files for analysis. All peaks should be sorted by the user
design - Choose the file with the experiment design information. CSV format
toppeak - The number of top peaks used for motif analysis. Default is allDesign file
The following columns are necessary, must be named as in template. An design file template can be downloaded HERE
SampleID
The id of the sample. This will be the header in output files, please make sure it is concise
Tissue
Tissue of the sample
Factor
Factor of the experiment
Condition
This is the group that will be used for pairwise differential expression analysis
Replicate
Replicate id
Peaks
The file name of the peak file for this sample
bamReads
The file name of the IP BAM for this sample
bamControl
The file name of the control BAM for this sample
ContorlID
The id of the control sample
PeakCaller
The peak caller usedCredits
This example worklow is derived from original scripts kindly contributed by the Bioinformatic Core Facility (BICF), Department of Bioinformatics