ChIPseq_PE
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.
- Author(s):
- Release: 0.12
- License: MIT
- UniqueID: 1834d09c-c683-4424-bc8d-57df156c2fc8
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).
- normalize_profile: Whether you want to have a profile normalized as Signal to Million Fragments.
Processing
- The workflow will remove illumina adapters and low quality bases and filter out any pair with mate smaller than 15bp.
- The filtered reads are mapped with bowtie2 with default parameters.
- The BAM is filtered to keep only MAPQ30 and concordant pairs.
- The peaks are called with MACS2 which at the same time generates a coverage file (normalized or not).
- The coverage is converted to bigwig.
- A MultiQC is run to have an overview of the QC.
Warning
- The filtered bam still has PCR duplicates which are removed by MACS2.
Contribution
@lldelisle wrote the workflow.
@nagoue updated the tools, made it work in usegalaxy.org, fixed the best practices and wrote the tests.