Snakemake pipeline for ATAC-Seq

public 1yr ago Version: v1.0.0 0 bookmarks

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Snakemake Workflow for ATAC-Seq

A snakefile pipeline for ATAC-Seq.

Change the config.yaml file appropriately according to your data. Update replicate1.tsv and replicate2.tsv for Replicates 1 and Replicates 2 respectively. Update parameters of Genrich in the config file.

Then run: snakemake -jnumber_of_cores, for example for 5 cores use:

snakemake -j5

and for a dry run use:

snakemake -j1 -n

and to print the commands in a dry run use:

snakemake -j1 -n -p

To use another config file use:

snakemake -j1 -p --configfile configfilehere.yaml

For the sake reproducibility, use conda to pull same versions of tools. Snakemake and conda have to be installed in your system:

snakemake --cores --use-conda

Citation

If you use this pipeline, please cite us as follows:

Sherine Awad. (2022). SherineAwad/ATAC-Seq: v1.0.0 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.5939988

Code Snippets

shell: 
  """
  trim_galore --gzip --retain_unpaired --trim1 --fastqc --fastqc_args "--outdir fastqc" -o galore --paired {input.r1} {input.r2}
  """

SnakeMake FastQC Trim_Galore From line 33 of master/Snakefile

shell:
    "bowtie2 -x {params} -1 {input.r1} -2 {input.r2} -S {output}"

SnakeMake Bowtie 2 From line 49 of master/Snakefile

shell:
    """
    mkdir -p galore
    mkdir -p fastqc
    trim_galore --gzip --retain_unpaired --trim1 --fastqc --fastqc_args "--outdir fastqc" -o galore {input}
    """

SnakeMake FastQC Trim_Galore From line 60 of master/Snakefile

shell:
   "bowtie2 -x {params.genome} -U {input} -S {output}"

SnakeMake Bowtie 2 From line 76 of master/Snakefile

shell:
    "samtools view {input[0]} -S -b > {output[0]}"

SnakeMake SAMtools From line 87 of master/Snakefile

shell: 
   "samtools sort -T {params} -n -o {output} {input}"

SnakeMake SAMtools From line 100 of master/Snakefile

shell:
   """
   Genrich -t {params[0]} -o {output[0]} -b {params[3]} -r -j -v -e {params[2]}  -q {params[5]} -a {params[6]} -l {params[7]}
   Genrich -t {params[1]} -o {output[1]} -b {params[4]} -r -j -v -e {params[2]}  -q {params[5]} -a {params[6]} -l {params[7]}
   bedtools intersect -a {params[3]} -b {params[4]} > intersect.out 
   bedtools subtract -a  {params[3]} -b {params[4]} > subtract.out 
   """  