.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH FASTAQ_TO_TILING_BAM "1" "October 2014" "Fastaq" "Fastaq executables"
.SH NAME
fastaq_to_tiling_bam
.SH DESCRIPTION
 fastaq_to_tiling_bam [options] <fasta/q in> <read length> <read step> <read prefix> <out.bam>
.PP
Takes a fasta/q 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\-\-read_group\fR READ_GROUP
Add the given read group ID to all reads [42]
.PP
Important: assumes that samtools is in your path


.SH "AUTHOR"
.sp
fastaq_to_tiling_bam was originally written by Martin Hunt (mh12@sanger.ac.uk)

.SH "COPYING"
.sp
Wellcome Trust Sanger Institute Copyright \(co 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version\&.