FASTAQ-TO_TILING_BAM

NAME

fastaq_to_tiling_bam - Make a BAM file of reads uniformly spread across the input reference

DESCRIPTION

usage: fastaq_to_tiling_bam [options] <infile> <read_length> <read_step> <read_prefix> <outfile>

Takes a sequence 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

options:

-h, --help

show this help message and exit

--qual_char QUAL_CHAR

Character to use for quality score [I]

--read_group READ_GROUP

Add the given read group ID to all reads [42]

Important: assumes that samtools is in your path