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Applied Genomics

ATAC-Seq Data Analysis

GitHub Classroom Assignment

ATAC-Seq Data Analysis Galaxy Tutorial

Tutorial1

In addition to the steps in the tutorial, run MultiQC on the FastQC results.

Criteria

In the end you should commit/upload to GitHub

  1. MultiQC Report with FastQC
  2. Heatmap for Genes
  3. Heatmap for CTCF peaks
  4. pyGenomeTracks

Link to them in the README

nf-core/atacseq

Redo the analysis using nf-core in a GitHub codespace

samplesheet.csv
sample,fastq_1,fastq_2,replicate
chr22_enriched,https://zenodo.org/record/3862793/files/SRR891268_chr22_enriched_R1.fastq.gz,https://zenodo.org/record/3862793/files/SRR891268_chr22_enriched_R2.fastq.gz,1
nf-params.json
{
  "input": "samplesheet.csv",
  "outdir": "results",
  "read_length": 50,
  "fasta": "https://hgdownload.cse.ucsc.edu/goldenpath/hg38/chromosomes/chr22.fa.gz",
  "gtf": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.ncbiRefSeq.gtf.gz",
  "aligner": "bowtie2",
  "max_cpus":   4,
  "max_memory": "14.GB",
  "max_time":   "6.h"
}
Run nf-core/atacseq
nextflow run nf-core/atacseq -r 2.1.2 -profile docker -params-file nf-params.json -resume

Criteria

  1. Upload the MultiQC report to GitHub
  2. Upload the plot at results/bowtie2/merged_library/deeptools/plotprofile/chr22_enriched_REP1.mLb.clN.scale_regions.plotHeatmap.pdf

Footnotes

  1. Lucille Delisle, Maria Doyle, Florian Heyl, ATAC-Seq data analysis (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/tutorial.html Online; accessed Mon Jul 15 2024 ↩