pyatac

The pyatac command line function contains several subcommands. To run a subcommand, run pyatac subcommand .... The available subcommands are:

To see available subcommands, you can also run pyatac --help. For each subcommand, options can be viewed as pyatac subcommand --help.

pyatac ins makes a bedgraph file with insertion frequencies for every base.

If a bedfile is provided, insertion track will only span regions in bedfile. Otherwise track will span whole genome.

Output: A tabix-indexed bedgraph file with insertion densities.

pyatac bias computes a bias track.

If a bedfile is provided, bias track will only span regions in bedfile. Otherwise track will span whole genome.

Output: A tabix-indexed bedgraph file with relative Tn5 preferences. These preferences are in log space.

pyatac vplot generates a vplot around sites in input bed file.

Output: An eps file with vplot image as well as a text file with vplot data.

pyatac bias_vplot computes the vplot based on the sequence bias and the global fragment size distribution

Output: An eps file with vplot image as well as a text file with vplot data.

pyatac sizes computes the fragment size distribution

Output: text file with sizes information

pyatac pwm computes the relative nucleotide frequencies around sites

Output: text file with PWM information

pyatac nucleotide computes the nucleotide frequencies around sites in the input bedfile

Output: text file with frequencies