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:
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
1) Annotate all peaks using ChipSeeker
2) Qulity control and signal profiling with Deeptools
2) Qulity control and signal profiling with Deeptools
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5) Using MEME-ChIP in motif finding for both original peaks and differently expressed peaks
5) Using MEME-ChIP in motif finding for both original peaks and differently expressed peaks
##Workflow Parameters
## Annotations 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 browser
## Workflow Parameters
bam - Choose all ChIP-seq alignment files for analysis.
bam - Choose all ChIP-seq alignment files for analysis.
genome - Choose a genomic reference (genome).
genome - Choose a genomic reference (genome).
peaks - Choose all the peak files for analysis. All peaks should be sorted by the user
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 all
toppeak - The number of top peaks used for motif analysis. Default is all
design - This file contains the experiment design information. CSV format
## Design file
The following columns are necessary, must be named as in template. An design file template can be downloaded [HERE](https://git.biohpc.swmed.edu/bchen4/chipseq_analysis/raw/master/docs/design_example.csv)
The following columns are necessary, must be named as in template. An design file template can be downloaded [HERE](https://git.biohpc.swmed.edu/bchen4/chipseq_analysis/raw/master/docs/design_example.csv)
