ChIP-seq

macs2_callpeak ^*

Authors

Menachem Sklarz

Affiliation

Bioinformatics core facility

Organization

National Institute of Biotechnology in the Negev, Ben Gurion University.

A module for running macs2 callpeak:

Requires

• bam files in the following slots:

  • sample_data[<sample>]["bam"]

• If using control (input) samples, make sure you include a sample-control table in your sample file.

Output

• Puts output macs2 output files in the following slots:

  • self.sample_data[<sample>]["prefix"])

  • self.sample_data[<sample>]["peak_bed"])

  • self.sample_data[<sample>]["peak_xls"])

  • self.sample_data[<sample>]["summit_bed"])

• If --bdg (or -B) was specified, puts output bdg files in the following slots:

  • self.sample_data[<sample>]["control_lambda"] - Control BedGraph

  • self.sample_data[<sample>]["treat_pileup"] - Treatment BedGraph

  • self.sample_data[<sample>]["bdg"] - Treatment BedGraph

  • self.sample_data[<control>]["bdg"] - Control BedGraph

• If bedToBigBed_path was specified, puts output bigbed files in the following slots:

  • self.sample_data[<sample>]["bb"]

• If getfasta was specified, puts output fasta files in the following slots:

  • self.sample_data[<sample>]["peak_fasta"]

  • self.sample_data[<sample>]["fasta.nucl"]

Parameters that can be set

Parameter	Values	Comments
bedToBigBed_path	path to bedToBigBed	Runs bedToBigBed to convert the peak bed files into bigbed for uploading to UCSC.
chrom.sizes	path to chrom.sizes for reference genome	If running bedToBigBed, you must supply the genome chrom.sizes file.
getfasta		If set, a fasta file containing the peak sequences will be produced.

Lines for parameter file

macs1_CP:
    module: macs2_callpeak
    base: samtools1
    script_path: /path/to/bin/macs2 callpeak
    bedToBigBed_path: /path/to/kentUtils/bin/bedToBigBed
    chrom.sizes: /path/to/genome.chrom.sizes
    getfasta: /path/to/bedtools getfasta -name -s
    redirects:
        --SPMR: 
        --bdg: 
        -g:     mm
        --bw:   400

References

Feng, J., Liu, T., Qin, B., Zhang, Y. and Liu, X.S., 2012. Identifying ChIP-seq enrichment using MACS. Nature protocols, 7(9), pp.1728-1740.

macs2_bdgcmp

Authors

Menachem Sklarz

Affiliation

Bioinformatics core facility

Organization

National Institute of Biotechnology in the Negev, Ben Gurion University.

A module for running macs2 bdgcmp:

Requires

• Files in the following slots:

  • self.sample_data[<sample>]["control_lambda"] - Control BedGraph

  • self.sample_data[<sample>]["treat_pileup"] - Treatment BedGraph

Output

• Puts output macs2 output files in the following slots:

  • self.sample_data[<sample>]["bdg"]) - The comparison bedgraph!

  • self.sample_data[<sample>]["bigwig"]) - if slop_path and ucscTools_path were passed

  • self.sample_data[<sample>]["wig"]) - if slop_path and ucscTools_path were passed

  • self.sample_data[<sample>]["tdf"]) - in TDF format (if slop_path, ucscTools_path and toTDF_path were passed)

Parameters that can be set

Parameter	Values	Comments
slop_path	path to bedtools slop	Is part of the process for converting bdg files into bigwig and wig
ucscTools_path	path to ucscTools	UCSCtools bedClip, bedGraphToBigWig and bigWigToWig are part of the process for converting bdg files into bigwig and wig
toTDF_path	path to toTDF	Converts the wig file into TDF file.
genome	path to chrom.sizes for reference genome	If running bedToBigBed, you must supply the genome chrom.sizes file.

Lines for parameter file

bdgcmp:
    module: macs2_bdgcmp
    base: macs1
    script_path: /path/to/macs2 bdgcmp
    genome: /path/to/chrom.sizes.txt
    slop_path: /path/to/bin/bedtools slop
    ucscTools_path: /path/to/ucscTools/bin
    toTDF_path: /path/to/bin/java -Xmx1500m -jar /path/to/igvtools.jar toTDF
    redirects:
        --method: FE

References

Feng, J., Liu, T., Qin, B., Zhang, Y. and Liu, X.S., 2012. Identifying ChIP-seq enrichment using MACS. Nature protocols, 7(9), pp.1728-1740.

CEAS

Authors

Menachem Sklarz

Affiliation

Bioinformatics core facility

Organization

National Institute of Biotechnology in the Negev, Ben Gurion University.

A module for running CEAS:

Requires

• Files in the following slots:

  • self.sample_data[<sample>]["peak_bed"] - Sample peak_bed file

  • self.sample_data[<sample>]["wig"] - An appropriate wig file

Output

• Puts CEAS output files in the following slots:

  • sample_data[sample]["CEAS.xls"]

  • sample_data[sample]["CEAS.R"]

  • sample_data[sample]["CEAS.plots"]

Parameters that can be set

Lines for parameter file

CEAS1:
    module: CEAS
    base: UCSC_BW_to_wig
    script_path: /path/to/bin/ceas
    redirects:
        -g: /path/to/hg19.refGene

References

Shin, H., Liu, T., Manrai, A.K. and Liu, X.S., 2009. CEAS: cis-regulatory element annotation system. Bioinformatics, 25(19), pp.2605-2606.