CUT&RUN (and CUT&TAG) Workflow

Inputs dataset

• The workflow needs a single input which is a list of dataset pairs of fastqsanger.

Inputs values

• adapter sequences: this depends on the library preparation. Usually CUT&RUN is Truseq and CUT&TAG is Nextera. If you don't know, use FastQC to determine if it is Truseq or Nextera
• reference_genome: this field will be adapted to the genomes available for bowtie2
• effective_genome_size: this is used by macs2 and may be entered manually (indications are provided for heavily used genomes)

Processing

• The workflow will remove illumina adapters and low quality bases and filter out any read smaller than 15bp
• The filtered reads are mapped with bowtie2 allowing dovetail and fragment length up to 1kb
• The BAM is filtered to keep only MAPQ30 and concordant pairs
• The PCR duplicates are removed with Picard
• The BAM is converted to BED to enable macs2 to take both pairs into account
• The peaks are called with macs2 which at the same time generates a coverage file.
• The coverage file is converted to bigwig
• A multiQC is run to have an overview of the QC

Warning

• The coverage output is not normalized.