.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH FASTAQ-TO_TILING_BAM "1" "February 2017" "fastaq 3.15.0" "User Commands"
.SH NAME
fastaq_to_tiling_bam \- Make a BAM file of reads uniformly spread across the input reference
.SH DESCRIPTION
usage: fastaq_to_tiling_bam [options] <infile> <read_length> <read_step> <read_prefix> <outfile>
.PP
Takes a sequence file. Makes a BAM file containing perfect (unpaired) reads
tiling the whole genome
.SS "positional arguments:"
.TP
infile
Name of input fasta/q file
.TP
read_length
Length of reads
.TP
read_step
Distance between start of each read
.TP
read_prefix
Prefix of read names
.TP
outfile
Name of output BAM file
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-qual_char\fR QUAL_CHAR
Character to use for quality score [I]
.TP
\fB\-\-read_group\fR READ_GROUP
Add the given read group ID to all reads [42]
.PP
Important: assumes that samtools is in your path