ChIP-seq peak-calling and differential analysis pipeline.
Type: Nextflow
Creators: Philip Ewels, Espinosa-Carrasco J, Patel H, Wang C, Ewels P
Submitter: WorkflowHub Bot
This workflow takes as input SR BAM from ChIP-seq. It calls peaks on each replicate and intersect them. In parallel, each BAM is subsetted to smallest number of reads. Peaks are called using both subsets combined. Only peaks called using a combination of both subsets which have summits intersecting the intersection of both replicates will be kept.
This workflow takes as input a collection of paired fastqs. Remove adapters with cutadapt, map pairs with bowtie2. Keep MAPQ30 and concordant pairs. MACS2 for paired bam.
This workflow takes as input a collection of fastqs (single reads). Remove adapters with cutadapt, map with bowtie2. Keep MAPQ30. MACS2 for bam with fixed extension or model.
ChIP-seq paired-end Workflow
Inputs dataset
- The workflow needs a single input which is a list of dataset pairs of fastqsanger.
Inputs values
- adapters sequences: this depends on the library preparation. 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).
...