QC check of raw .fastq files using FASTQC.
RAW_DATA_DIR:
QC_PATH:
FASTQC_VERSION:
Runs Homer Tools to trim adapters from .fastq files.
ENDS:
RAW_DATA_DIR:
HOMER_TRIM_OPTIONS:
TRIMMED_DATA_PATH:
HOMER_VERSION:
Runs Bowtie to align .fastq files.
ENDS:
TRIMMED_DATA_PATH:
BOWTIE_OPTIONS:
BOWTIE_INDEX:
BOWTIE_RESULTS:
BOWTIE_VERSION:
SAMTOOLS_VERSION:
BEDTOOLS_VERSION:
Runs HOMER to visualize read density from ChIPseq data.
BOWTIE_RESULTS:
CHROM_SIZES:
HOMER_RESULTS:
HOMER_VERSION:
TEMP_DIR:
Runs HOMER to call peaks from ChIPseq data.
PAIR_LIST:
HOMER_RESULTS:
HOMER_PEAKS_OPTIONS:
HOMER_VERSION:
TEMP_DIR:
Runs HOMER to create peak track from ChIPseq data.
PAIR_LIST:
HOMER_RESULTS:
HOMER_VERSION:
TEMP_DIR:
Runs HOMER to annotate peak track from ChIPseq data.
PAIR_LIST:
HOMER_RESULTS:
HOMER_VERSION:
TEMP_DIR:
HOMER_GENOME:
HOMER_ANNOTATE_OPTIONS:
Runs HOMER to find motifs from ChIPseq data.
PAIR_LIST:
HOMER_RESULTS:
HOMER_VERSION:
TEMP_DIR:
HOMER_GENOME:
HOMER_MOTIFS_OPTIONS: