detect#

Compute per-nucleotide cleavage deviation statistics

INTERVAL_FILE is a BED-formatted file contained genomic regions to be analyzed. BAM_FILE is the path to a BAM-format tag alignment file. FASTA_FILE is the path to genome FASTA file (requires associated FASTA index in same folder (see documentation on how to create an index).

Per-nucleotde statistics are written to a bedGraph file: <outprefix>.bedgraph). Footprints are optionally written to a BED3-format file: <outprefix>.fdr<thresh>.bed). Footprint FDR threshold(s) can be specified using the --write_footprints option. Output file column definitions are written to a header within each file.

detect [OPTIONS] INTERVAL_FILE BAM_FILE FASTA_FILE

Options

--bias_model_file <bias_model_file>#: Use a k-mer model for sequence bias (supplied by file). If argument is not provided the model defaults to uniform sequence bias.

--half_win_width <half_win_width>#

Half window width to apply bias model

Default: 5

--smooth_half_win_width <smooth_half_win_width>#

Half window width to apply smoothing model. When set to 0, no smoothing is applied.

Default: 50

--smooth_clip <smooth_clip>#

Fraction of bases to clip when computing trimmed mean in the smoothing window

Default: 0.01

--dispersion_model_file <dispersion_model_file>#: Dispersion model for negative binomial tests. If argument is not provided then no stastical output is provided. File is in JSON format and generated using the command learn_dm

--fdr_shuffle_n <fdr_shuffle_n>#

Number of times to shuffle data for FDR calculation

Default: 100

--min_qual <min_qual>#

Ignore reads with mapping quality lower than this threshold

Default: 1

--keep_dups <keep_dups>#

Keep duplicate reads

Default: True

--keep_qcfail <keep_qcfail>#

Keep QC-failed reads

Default: False

--outprefix <outprefix>#

Output prefix

Default: out

--write_footprints <write_footprints>#

Output footprints at specified FDRs

Default: 0.001,0.01,0.05

--bam_offset <bam_offset>#

BAM file offset (enables support for other datatypes – e.g. Tn5/ATAC)

Default: 0,-1

--seed <seed>#: Seed for random number generator – set for reproducible results

--n_threads <n_threads>#

Number of processors to use

Default: 2

--batch_size <batch_size>#

Batch size of intervals to process

Default: 100

Arguments

INTERVAL_FILE#: Required argument

BAM_FILE#: Required argument

FASTA_FILE#: Required argument

Command reference

learn_beta