fastaq_to_tiling_bam (1)

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

fastaq_to_tiling_bam was originally written by Martin Hunt ([email protected])

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.