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Commit b478c843 authored by Holly Ruess's avatar Holly Ruess
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fixed README

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1 merge request!2Resolve "Remove unnecessary columns from design file"
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# Astrocyte ATAC-seq analysis Workflow Package
[![Build Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/master/build.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/commits/master)
[![Coverage Report](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/master/coverage.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/commits/master)
[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.24.0-brightgreen.svg
)](https://www.nextflow.io/)
[![Astrocyte](https://img.shields.io/badge/astrocyte-%E2%89%A50.1.0-blue.svg)](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html)
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
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