ChIP-seq Modules – HOMER¶
FASTQC¶
- omics_pipe.modules.fastqc.fastqc(sample, fastqc_flag)[source]¶
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)[source]¶
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)[source]¶
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)[source]¶
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)[source]¶
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)[source]¶
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)[source]¶
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)[source]¶
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: