Pipeline_ChIP_and_ATAC

Requried software

• sra-tools https://github.com/ncbi/sra-tools
• fastqc https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
• multiqc https://multiqc.info/
• cutadapt
• bowtie2
• samtools
• macs2
• bedtools
• bedGraphToBigWig https://www.encodeproject.org/software/bedgraphtobigwig/

Walkthrough

It is recommended to start with a Projectdir/src directory where all the used snakemake, config, qsub files go (without subdirectories) and a subdriectory called "rules" with the used snakemake rules. The rest of the structure will be build by the snakemake scripts. Of course you can use another structure but then you have to go through all the path definitions and input and output fields of the snakemake rules.

Data download

If you need do download published data sets from NCBI with sra number:

• You need to install
  • sra-tools
• Use the dir Download_NCBI_data
  • Edit the config files as written in the comments
  • either use the .py file or the cluster script and edit it as written in the comments

If you have the sequencing data in your local network it is recommended to copy the data files to your working directory:

• Use the dir Copy_local_seq_data_to_projectdirect

  • Edit the config files as written in the comments
  • you can then run snakemake_copy_data_from_local.py either within the terminal or as a cluster job

• If you did the setup as described and ran the data-scripts you should end up with this file structure:

  • Projectdirectory:
    * src * rules * config_files.yaml * snakemake_files.py * qsub_files.sh * data * datafiles

Quality control

• You need to install
  • fastqc
  • multiqc
• put qsub_fastqc_multiqc.sh to /src and run it
• from the multiqc.html figure out if it identified any adapter sequences

Processing

• choose:
  • ChIP_single_end_src_dir for ChIP single-end data
  • ATAC_paired_end_src_dir for ATAC, paired-end data
• Edit the config file as written in the comments, you could also use (or copy paste) the config file from the data download and just add the section for "adapters:" and "bigWigs"
• Edit the snakemake file as written in the comments
• Edit the qsub file as written in the comments

Reference Genome

Those examples are based on te danRer11 reference genome. You need to index your genome and insert the path to it in the snakemake files.

If you use a different reference genome you would have to adjust "params:" in "rule sub2bigWig", "rule bdg2bigWig" and "rule bdg2bigWigCtl" in the "generatingBigWig.smk"