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, (2) Peak annotation, (3) Differential peak analysis, and (4) motif analysis. BAM files and SORTED peak BED files selected as input. For each file 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 peaks##Workflow 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
toppeak - The number of top peaks used for motif analysis. Default is all
design - This file contains the experiment design information. CSV formatThe following columns are necessary, must be named as in template and can be in any order:
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 usedTest Data
Credits
This example worklow is derived from original scripts kindly contributed by the Bioinformatic Core Facility (BICF), Department of Bioinformatics