General workflow

It is advised not to mix ChIP-seq experiments using different anybodies in the same snakemake workflow. In other words, every ChIP-seq experiment with a specific antibody should get its own snakemake workflow.

Naming requirements

In config.yaml

It is important that values of samples matchkeys of units; for example, consider the following units entries

units:
    control_WT_rep1:
    	- reads_R1.fastq.gz
        - reads_R2.fastq.gz

Then there needs to be a matching value control_WT_rep1 in samples. e.g.

samples:
    WT:
        control:
            - control_WT_rep1

Notice also that the keys WT and control have to match samplea key.

The general format is

samples:
    <CONDITION1>:
        control:
            - control_<CONDITION1>_<REPLICATE>
            - ...
        IP:
            - IP_<CONDITION1>_<REPLICATE>
            - ...
    <CONDITION2>:
        control:
            - control_<CONDITION2>_<REPLICATE>
            - ...
        IP:
            - IP_<CONDITION2>_<REPLICATE>
            - ...
    ...

How to get started

Changes to config.yaml to reflect the actual experiment design and input files

Samples

Change samples and units (see the previous section for naming requirements)

deeptools parameters

• Confirm ignore_for_normalisation entries

• Set binsize for BigWig plots

• Specify scale_method which must be one of ["readCount", "SES", "None"]

• Adjust bamCompare_specific_args; e.g. arguments pertaining to the scaling should go here, e.g.

  deeptools:
      ...
      scale_method: "SES"
      bamCompare_specific_args:
          - "--sampleLength 2000"
      ...

A note on scaling
Which scaling method is best depends on the data and requirements. For example, if coverage is low scale_method: "SES" (which corresponds to --scaleFactorsMethod SES in bamCompare) might not work, or might require a larger bamCompare --sampleLength value. In that case, the readCount scaling method may be used

deeptools:
    ...
    scale_method: "readCount"
    bamCompare_specific_args:
    ...

macs2 parameters

• Adjust the format of the input files; for paired-end data

  macs2:
      ...
      format: "BAMPE"

  For single end data

  macs2:
      ...
      format: "BAM"

  From the MACS2 Usage

  Format of tag file can be ELAND, BED, ELANDMULTI, ELANDEXPORT, ELANDMULTIPET (for pair-end tags), SAM, BAM, BOWTIE, BAMPE or BEDPE. Default is AUTO which will allow MACS to decide the format automatically. AUTO is also useful when you combine different formats of files. Note that MACS can't detect BAMPE or BEDPE format with AUTO, and you have to implicitly specify the format for BAMPE and BEDPE.