Execute CUT&RUN chromatin mapping pipelines
pipeline-cutandrunskillsetup L4★35
ammawla/encode-toolkit ↗What it does
Execute CUT&RUN processing pipeline from FASTQ to
Best for
Processing CUT&RUN epigenomic data with targeted chromatin profiling.
Inputs
- · FASTQ files (paired-end or single-end)
- · Aligned BAM files
Outputs
- · Peak calls (narrowPeak/broadPeak format)
- · Signal tracks (bigWig)
- · Quality control report
Requires
- · Nextflow
- · Docker
- · BWA/Bowtie2 aligner
- · MACS2 peak caller
Preconditions
- · Reference genome indexed
- · FASTQ files available
- · Nextflow/Docker installed
Failure modes
- · Poor FASTQ quality (low pass rate)
- · Reference genome mismatch
- · Memory exhaustion on large datasets
- · Adapter contamination
Trust signals
- · ENCODE consortium standards documented
- · Maintained in ammawla/encode-toolkit
- · Peer-reviewed publications cited
- · Citable references provided