Quickstart Guide¶

This gives a quick overview of running spats. For more detail, see the spats_tool documentation or the detailed options.

First, create a folder for your experiment, and run spats_tool init:

$ mkdir testing_2017_08_10
$ cd testing_2017_08_10
$ spats_tool init

This creates a default spats.config file. The minimum required options for this file are as follows:

[spats]
target = my_target.fa
r1 = /path/to/data/experiment_data_R1.fastq.gz
r2 = /path/to/data/experiment_data_R2.fastq.gz

See the run.Run documentation for detailed information about all available options.

You may now wish to do a reads analysis:

$ spats_tool reads

Use spats_tool dump reads to dump the data for the reads analysis to reads.csv.

The basic command is spats_tool run, which performs the SPATS run to compute site reactivities:

$ spats_tool run

Use spats_tool dump run to dump the data for the run to CSV files.

For more details, see the spats_tool documentation or the detailed options.

Spats