ChIP Peak Calling

Info

For all ChIP datasets we will follow more or less the protocol from the Blueprint Consortia.

Versions (2020-07-22)

• 01: Inital version, trimming optional obsolete
• 02: Sara version 2, same as 01, except mapping filtering (q15) optional
• 03: Sara version 3, same as 02, except experiment/input included

Workflow

The alignment scripts perform the following steps:

• [optional] Trim Illumina adaptor and quality (Cutadapt)
• Align given FASTQ file(s) using SAMPLE_NAME to GENOME (Burrow-Wheeler Aligner (bwa))
• Mark duplicates using GATK4 MarkDuplicates, do not remove duplicates, just mark
• filter alignments upon MAPQ (samtools), default q=15
• Compute average feature density over a specified window size using deepTools,bamCoverage
• for SE data only: determine predominant fragment length using run_spp.R from (PhantomPeakQualTools)
• run Peak Calling (MACS2) in both narrow and broad mode.

ToDo

• drink a beer ...