--bamfiles Only process BAM files
--bedtools_path path to BEDTools executable (leave blank if in path)
--bins Width of bins to use for mapping reads
[Current value: 75]
--bowtie Perform bowtie2 alignment [1/0]
[Current value: 1]
--bowtie2_add_flags Additional flags to use for bowtie2 alignment
--bowtie2_genome_dir Directory and basename for bowtie2 .bt2 indices
--bowtie2_path path to bowtie2 executable (leave blank if in path)
--dam Specify file to use as Dam control
--extend_reads Perform read extension [1/0]
[Current value: 1]
--extension_method Read extension method to use; options are:
full: Method used by version 1.3 and earlier. Extends all reads to the value set with --len.
gatc: Default for version 1.4 and above. Extends reads to --len or to the next GATC site, whichever is shorter. Using this option increases peak resolution.
[Current value: gatc]
--full_data_files Output full binned ratio files (not only GATC array)
--gatc_frag_file GFF file containing all instances of the sequence GATC
--just_align Just align the FASTQ files, generate BAM files, and exit
--kde_plot create an Rplot of the kernel density fit for normalisation (requires R)
--keep_original_bams Keep unextended BAM files if using single-end reads
--len Length to extend reads to
[Current value: 300]
--load_defaults Load this saved set of defaults
(use 'list' to list current saved options)
--max_norm_value Maximum log2 value to limit normalisation search at (default = +5)
[Current value: 5]
--method_subtract Output values are (Dam_fusion - Dam) instead of log2(Dam_fusion/Dam) (not recommended)
--min_norm_value Minimum log2 value to limit normalisation search at (default = -5)
[Current value: -5]
--no_file_filters Do not trim filenames for output
[Current value: 1]
--norm_method Normalisation method to use; options are:
kde: use kernel density estimation of log2 GATC fragment ratio (default)
rpm: use readcounts per million reads (not recommended for most use cases)
rawbins: new experimental method, may be more accurate
[Current value: kde]
--norm_override Normalise by this amount instead
--norm_steps Number of points in normalisation routine (default = 300)
[Current value: 300]
--out_name Use this as the fusion-protein name when saving the final ratio
--output_format Output tracks in this format [gff/bedgraph]
[Current value: bedgraph]
--paired Process paired-end reads (experimental, use with caution)
--ps_debug Print extra debugging info on pseudocount calculations in log file
--ps_factor Value of c in c*(reads/bins) formula for calculating pseudocounts (default = 10)
[Current value: 10]
--pseudocounts Add this value of psuedocounts instead (default: optimal number of pseudocounts determined algorithmically)
--q Cutoff average Q score for aligned reads
[Current value: 30]
--qscore1max max decile for normalising from Dam array
[Current value: 1]
--qscore1min min decile for normalising from Dam array
[Current value: 0.4]
--qscore2max max decile for normalising from fusion-protein array
[Current value: 0.9]
--reset_defaults Delete user-defined parameters
--samtools_path path to samtools executable (leave blank if in path)
--save_defaults Save runtime parameters as default
(provide a name to differentiate different genomes -- these can be loaded with 'load_defaults')
--threads threads for bowtie2 to use
[Current value: 7]
--write_raw Write TSV file with raw counts for each Dam, sample pair