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fastaq-to_tiling_bam - Online in the Cloud

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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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