CLI arguments

epiout

epiout [OPTIONS]

Options

--bed <bed>: Required bed file containing accessible regions

--alignments <alignments>: Required file containing bam files for each samples. Either each line is bam file (Ex: a.bam b.bamc.bam) or first columns is sample and second column is path to bam Ex: (a a.bam b b.bam c c.bam)

--output_prefix <output_prefix>: Required Output prefix for {prefix}.raw_counts.csv, {prefix}.counts.csv, {prefix}.bed

--cores <cores>: Number of cores to use for paralell counting.

--mapq <mapq>: Minimum read quality of reads.

--min_count <min_count>: Minimum count at least one sample.

--min_percent_sample <min_percent_sample>: minimum percentange of sample peak with at least one read.

--subset_chrom: Subset chr1 to 22 and X,Y

--file_format <file_format>: File format of count table

epiout

epiout [OPTIONS]

Options

--count_table <count_table>: Required Path to count table csv containing peaks (rows) x samples (columns)

--output_prefix <output_prefix>: Required Output prefix for {prefix}.h5ad and and {prefix}.result.csv.

--confounders <confounders>: Known confounding factors as tsv file where each row is a sample and each column is a confounding factor.

--bottleneck_size <bottleneck_size>: Predefined bottleneck size. If not provide, will be tuned.

--cores <cores>: Number of cores to use for paralell counting.

epiannot

epiannot [OPTIONS]

Options

--bed <bed>: Required bed file containing accessible regions to annotate

--config <config>: Required config file containing bed and hic files to annotate against

--output_prefix <output_prefix>: Required Output prefix for {prefix}.annotation.csv, {prefix}.contact.csv,`{prefix}.gtf.csv`, {prefix}.genes.csv files.

--gtf <gtf>: GTF files to obtain genes.

--chrom_sizes <chrom_sizes>: Chrom sizes files faidx {fasta} -i chromsizes > {chrom_sizes}

--counts <counts>: Path count table of accessible reads.

--gene_types <gene_types>: List of gene types separated by comma.

--hic_bin_vicinity <hic_bin_vicinity>: Number of bin distance between peaks to consider in conduct analysis.

--hic_normalization <hic_normalization>: Hic normalization method.

--hic_binsize <hic_binsize>: Hic bin size.

--hic_min_read <hic_min_read>: Minimum number of hic min reads to include

epiannot_create

epiannot_create [OPTIONS]

Options

--tissue <tissue>: Tissue, cell line, primiary or differentialed cell

--output_dir <output_dir>: Required Output directory of create config and download files

--tf: If include TF-ChIP-seq marks

--hic: If inclice Hi-C

--ccres: If include ccres

epiannot_list

List available tissues, cell lines, primary or differentiated cells.

epiannot_list [OPTIONS]