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differential_ATACseq.smk

Snakemake workflow for differential analysis of ATAC-seq data.

Note

Please make sure that you have Singularity and Snakemake installed on your system and cloned the SnakeNgs repository.

Workflow

differential_ATACseq.smk rulegraph

The rulegraph was created by snakevision.

  1. Merge peak resions from all samples using bedtools merge.
  2. Read count for each peak region using featureCounts.
  3. Differential analysis using DESeq2.

Usage

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snakemake -s /path/to/SnakeNgs/snakefile/differential_ATACseq.smk \
--config \
workdir=/path/to/output \
experiment_table=/path/to/experiment_table.tsv \
--cores <int> \
--use-singularity \
--rerun-incomplete
  • path/to/output is the directory where the output files will be saved.
  • path/to/experiment_table.tsv is a tab-separated file containing the following information:
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sample  bam peak    group
SRRXXXXXX   /path/to/SRRXXXXXX.sort.rmdup.bam   /path/to/SRRXXXXXX_peaks.narrowPeak Ref
SRRYYYYYY   /path/to/SRRYYYYYY.sort.rmdup.bam   /path/to/SRRYYYYYY_peaks.narrowPeak Ref
SRRZZZZZZ   /path/to/SRRZZZZZZ.sort.rmdup.bam   /path/to/SRRZZZZZZ_peaks.narrowPeak Ref
SRRAAAAAA   /path/to/SRRAAAAAA.sort.rmdup.bam   /path/to/SRRAAAAAA_peaks.narrowPeak Alt
SRRBBBBBB   /path/to/SRRBBBBBB.sort.rmdup.bam   /path/to/SRRBBBBBB_peaks.narrowPeak Alt
SRRCCCCCC   /path/to/SRRCCCCCC.sort.rmdup.bam   /path/to/SRRCCCCCC_peaks.narrowPeak Alt

It is expected that the input BAM files are generated by the preprocessing_ChIPseq.smk workflow and the peak files are generated by the callpeak_ATACseq.smk workflow.

Docker image used in the workflow