ChIPseq_SR
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.
- Author(s):
- Release: 0.12
- License: MIT
- UniqueID: fe6bda9f-1fc2-4a86-bf8d-e779c79466fc
ChIP-seq single-read Workflow
Inputs dataset
- The workflow needs a single input which is a list of fastqsanger files.
Inputs values
- adapters sequence_forward: 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 Reads.
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 with default parameters.
- The BAM is filtered to keep only MAPQ30.
- The peaks are called with MACS2 with a fixed extension of 200bp 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.