ATAC-Seq Data Analysis
GitHub Classroom Assignment
ATAC-Seq Data Analysis Galaxy Tutorial
In addition to the steps in the tutorial, run MultiQC on the FastQC results.
Criteria
In the end you should commit/upload to GitHub
- MultiQC Report with FastQC
- Heatmap for Genes
- Heatmap for CTCF peaks
- pyGenomeTracks
Link to them in the README
nf-core/atacseq
Redo the analysis using nf-core in a GitHub codespace
sample,fastq_1,fastq_2,replicatechr22_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
{ "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"}
nextflow run nf-core/atacseq -r 2.1.2 -profile docker -params-file nf-params.json -resume
Criteria
- Upload the MultiQC report to GitHub
- Upload the plot at
results/bowtie2/merged_library/deeptools/plotprofile/chr22_enriched_REP1.mLb.clN.scale_regions.plotHeatmap.pdf
Footnotes
-
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 ↩