ChIP-seq Modules – HOMER

FASTQC

omics_pipe.modules.fastqc.fastqc(sample, fastqc_flag)

QC check of raw .fastq files using FASTQC.

input:

.fastq file

output:

folder and zipped folder containing html, txt and image files

citation:

Babraham Bioinformatics

link:

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

parameters from parameters file:

RAW_DATA_DIR:

QC_PATH:

FASTQC_VERSION:

COMPRESSION:

ChIP trim

omics_pipe.modules.ChIP_trim.ChIP_trim(sample, ChIP_trim_flag)

Runs Homer Tools to trim adapters from .fastq files.

input:

.fastq file

output:

.fastq file

citation:

Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432

link:

http://homer.salk.edu/homer/

parameters from parameters file:

ENDS:

RAW_DATA_DIR:

HOMER_TRIM_OPTIONS:

TRIMMED_DATA_PATH:

HOMER_VERSION:

Bowtie

omics_pipe.modules.bowtie.bowtie(sample, bowtie_flag)

Runs Bowtie to align .fastq files.

input:

.fastq file

output:

sample.bam

citation:

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25

link:

http://bowtie-bio.sourceforge.net/index.shtml

parameters from parameters file:

ENDS:

TRIMMED_DATA_PATH:

BOWTIE_OPTIONS:

BOWTIE_INDEX:

BOWTIE_RESULTS:

BOWTIE_VERSION:

SAMTOOLS_VERSION:

BEDTOOLS_VERSION:

TEMP_DIR:

Read Density -HOMER

omics_pipe.modules.read_density.read_density(sample, read_density_flag)

Runs HOMER to visualize read density from ChIPseq data.

input:

.bam file

output:

.txt file

citation:

Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432

link:

http://homer.salk.edu/homer/

parameters from parameters file:

BOWTIE_RESULTS:

CHROM_SIZES:

HOMER_RESULTS:

HOMER_VERSION:

TEMP_DIR:

Peak Detection - HOMER

omics_pipe.modules.homer_peaks.homer_peaks(step, homer_peaks_flag)

Runs HOMER to call peaks from ChIPseq data.

input:

.tag input file

output:

.txt file

citation:

Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432

link:

http://homer.salk.edu/homer/

parameters from parameters file:

PAIR_LIST:

HOMER_RESULTS:

HOMER_PEAKS_OPTIONS:

HOMER_VERSION:

TEMP_DIR:

Peak Annotation & Visualization - HOMER

omics_pipe.modules.peak_track.peak_track(step, peak_track_flag)

Runs HOMER to create peak track from ChIPseq data.

input:

.tag input file

output:

.txt file

citation:

Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432

link:

http://homer.salk.edu/homer/

parameters from parameters file:

PAIR_LIST:

HOMER_RESULTS:

HOMER_VERSION:

TEMP_DIR:

omics_pipe.modules.annotate_peaks.annotate_peaks(step, annotate_peaks_flag)

Runs HOMER to annotate peak track from ChIPseq data.

input:

.tag input file

output:

.txt file

citation:

Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432

link:

http://homer.salk.edu/homer/

parameters from parameters file:

PAIR_LIST:

HOMER_RESULTS:

HOMER_VERSION:

TEMP_DIR:

HOMER_GENOME:

HOMER_ANNOTATE_OPTIONS:

Find Motifs - HOMER

omics_pipe.modules.find_motifs.find_motifs(step, find_motifs_flag)

Runs HOMER to find motifs from ChIPseq data.

input:

.txt peak file from Homer

output:

.txt file

citation:

Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432

link:

http://homer.salk.edu/homer/

parameters from parameters file:

PAIR_LIST:

HOMER_RESULTS:

HOMER_VERSION:

TEMP_DIR:

HOMER_GENOME:

HOMER_MOTIFS_OPTIONS: