DOKK / manpages / debian 11 / fastaq / fastaq-to_tiling_bam.1.en

FASTAQ-TO_TILING_BAM(1)

User Commands

FASTAQ-TO_TILING_BAM(1)

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

optional arguments:

-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

April 2020

fastaq 3.17.0