index.md

Astrocyte ATAC-seq 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 peaks

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.
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 all

Design file

• The Design file is a tab-delimited file with 4 columns for Single-End and 5 columns for Paired-End. Letter, numbers, and underlines can be used in the names. However, the names must begin with a letter. Columns must be as follows:

  sample_id The id of the sample. This will be the header in output files, please make sure it is concise experiment_id Same name given for all replicates of treatment. Will be used for the consensus header. replicate Replicate number fastq_read1 Name of fastq file 1 for SE or PE data fastq_read2 Name of fastq file 2 for PE data

• See HERE for an example design file, paired-end

• See HERE for an example design file, single-end

Common Errors

If you find an error, please let the BICF know and we will add it here.

Citation

Please cite individual programs and versions used HERE, and the pipeline doi: coming soon. Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).

Credits

This example worklow is derived from original scripts kindly contributed by the Bioinformatic Core Facility (BICF), in the Department of Bioinformatics.