This is the command fastaq-to_tiling_bam that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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