fastaq_to_tiling_bam1
Overview
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
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.