NAME
fastaq_to_tiling_bam
DESCRIPTION
fastaq_to_tiling_bam [options] <fasta/q in> <read length> <read step> <read prefix> <out.bam>
Takes a fasta/q file. Makes a BAM file containing perfect (unpaired) reads tiling the whole genome
positional arguments:
- infile
-
Name of input fasta/q file
- read_length
-
Length of reads
- read_step
-
Distance between start of each read
- read_prefix
-
Prefix of read names
- outfile
-
Name of output BAM file
optional arguments:
- -h, --help
-
show this help message and exit
- --read_group READ_GROUP
-
Add the given read group ID to all reads [42]
Important: assumes that samtools is in your path
AUTHOR
fastaq_to_tiling_bam was originally written by Martin Hunt ([email protected])
COPYING
Wellcome Trust Sanger Institute Copyright © 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.