FASTQ-SAMPLE

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
AUTHOR

NAME

fastq-sample - sample random reads from a fastq file

SYNOPSIS

fastq-sample [OPTION]... FILE [FILE2]

DESCRIPTION

Given a FASTQ file, random reads are sampled and output, with or without replacement, according to the ’-r’ option. The number of reads to sample can be specifed with the ’-n’ option, or in terms of the proportion of total reads using ’-p’ option.

If two files are given, the input is treated as paired-end, and matching pairs are sampled and output into seperate files: [prefix].1.fastq and [prefix].2.fastq, where [prefix] is set with the ’-o’ option.

OPTIONS

−n N

The number of reads to sample and output

−p N

The number of reads to sample in terms of the proportion of total reads. If sampling with replacement, this number may be greater than 1.0.

−o, −−output=PREFIX

The filename prefix to which output should be written. If single-end data is being sampled, the output file is [PREFIX].fastq, and with paired-end, [PREFIX].1.fastq and [PREFIX].2.fastq. (Default:

−r, −−with−replacement

Sample with replacement. (By default, sampling is done without replacement.)

−c, −−complement-output=PREFIX

Output reads not included in the random sample to a file (or files) with the given prefix. By default, these reads are not output.

−s, −−seed

Seed the random number generator. Using the same seed on the same data set will produce the same random sample.

−h, −−help

Output a help message and exit.

−V, −−version

Output version information and exit.

AUTHOR

Written by Daniel C. Jones <dcjones@cs.washington.edu>