https://github.com/kzkedzierska/atac

ATAC-seq snakemake pipeline
https://github.com/kzkedzierska/atac

atac-seq snakemake snakemake-workflow

Last synced: 3 months ago
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ATAC-seq snakemake pipeline

• Host: GitHub
• URL: https://github.com/kzkedzierska/atac
• Owner: kzkedzierska
• Created: 2019-04-15T13:52:18.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2023-04-04T18:41:02.000Z (about 2 years ago)
• Last Synced: 2025-01-18T08:36:28.042Z (5 months ago)
• Topics: atac-seq, snakemake, snakemake-workflow
• Language: Python
• Homepage:
• Size: 132 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# ATAC-seq analysis pipeline

ATAC-seq pipeline wrote in Snakemake. Work in progress ;)

## Prerequisites

I put the versions I'm using in brackets. 

* fastqc (0.11.8)

* multiqc (1.5.dev0)

* cutadapt (2.1)

* trim\_galore (0.5.0)

* bwa (0.7.17)

* samtools (1.7)

* picard (2.19.0)

* conda (4.7.5)

* macs2 (2.1.2)